pinecone/core-2020-05-10-deduplication huggingface dataset:
Influence of natural convection in a porous medium when producing from borehole heat exchangers

Convection currents in a porous medium form when the medium is subject to sufficient heating from below (or equivalently, cooling from above) or when cooled or heated from the side. In the context of geothermal energy extraction, we are interested in how the convection currents transport heat when a sealed borehole containing cold fluid extracts heat from the porous medium; also known as a borehole heat exchanger. Using pseudospectral methods together with domain decomposition, we consider two scenarios for heat extraction from a borehole; one system where the porous medium is initialized with constant temperature in the vertical direction and one system initialized with a vertical temperature gradient. We find the convection currents to have a positive effect on the heat extraction for the case with a constant initial temperature in the porous medium, and a negative effect for some of the systems with an initial temperature gradient in the porous medium: Convection gives a negative effect when the borehole temperature is close the initial temperature in the porous medium, but gradually provides a positive effect if the borehole temperature is decreased and the Rayleigh number is larger
Hydraulic validation of two-dimensional simulations of braided river flow with spatially continuous aDcp data

Gravel-bed braided rivers are characterized by shallow, branching flow across low relief, complex and mobile bed topography. These conditions present a major challenge for the application of higher dimensional hydraulic models, the predictions of which are nevertheless vital to inform flood risk and ecosystem management. This paper demonstrates how high-resolution topographic survey and hydraulic monitoring at a density commensurate with model discretization can be used to advance hydrodynamic simulations in braided rivers. Specifically, we detail applications of the shallow water model, Delft3d, to the Rees River, New Zealand, at two nested scales: a 300 m braid bar unit and a 2.5 km reach. In each case, terrestrial laser scanning was used to parameterize the topographic boundary condition at hitherto unprecedented resolution and accuracy. Dense observations of depth and velocity acquired from a mobile acoustic Doppler current profiler (aDcp), along with low-altitude aerial photography, were then used to create a data-rich framework for model calibration and testing at a range of discharges. Calibration focused on the estimation of spatially uniform roughness and horizontal eddy viscosity, ?H, through comparison of predictions with distributed hydraulic data. Results revealed strong sensitivity to ?H, which influenced cross-channel velocity and localization of high shear zones. The high resolution bed topography partially accounts for form resistance and the recovered roughness was found to scale by 1.2-1.4 D84 grain diameter. Model performance was good for a range of flows, with minimal bias and tight error distributions, suggesting acceptable predictions can be achieved with spatially uniform roughness and ?H.preprintPeer reviewe
The importance of hydraulic groundwater theory in catchment hydrology: the legacy of Wilfried Brutsaert and Jean-Yves Parlange

Based on a literature overview, this paper summarizes the impact and legacy of the contributions of Wilfried Brutsaert and Jean-Yves Parlange (Cornell University) with respect to the current state-of-the-art understanding in hydraulic groundwater theory. Forming the basis of many applications in catchment hydrology, ranging from drought flow analysis to surface water-groundwater interactions, hydraulic groundwater theory simplifies the description of water flow in unconfined riparian and perched aquifers through assumptions attributed to Dupuit and Forchheimer. Boussinesq (1877) derived a general equation to study flow dynamics of unconfined aquifers in uniformly sloping hillslopes, resulting in a remarkably accurate and applicable family of results, though often challenging to solve due to its nonlinear form. Under certain conditions, the Boussinesq equation can be solved analytically allowing compact representation of soil and geomorphological controls on unconfined aquifer storage and release dynamics. The Boussinesq equation has been extended to account for flow divergence/convergence as well as for nonuniform bedrock slope (concave/convex). The extended Boussinesq equation has been favorably compared to numerical solutions of the three-dimensional Richards equation, confirming its validity under certain geometric conditions. Analytical solutions of the linearized original and extended Boussinesq equations led to the formulation of similarity indices for baseflow recession analysis, including scaling rules, to predict the moments of baseflow response. Validation of theoretical recession parameters on real-world streamflow data is complicated due to limited measurement accuracy, changing boundary conditions, and the strong coupling between the saturated aquifer with the overlying unsaturated zone. However, recent advances are shown to have mitigated several of these issues. The extended Boussinesq equation has been successfully applied to represent baseflow dynamics in catchment-scale hydrological models, and it is currently considered to represent lateral redistribution of groundwater in land surface schemes applied in global circulation models. From the review, it is clear that Wilfried Brutsaert and Jean-Yves Parlange stimulated a body of research that has led to several fundamental discoveries and practical applications with important contributions in hydrological modeling
Review on airflow in unsaturated zones induced by natural forcings

Subsurface airflow in unsaturated zones induced by natural forcings is of importance in many environmental and engineering fields, such as environmental remediation, water infiltration and groundwater recharge, coastal soil aeration, mine and tunnel ventilation, and gas exchange between soil and atmosphere. This review synthesizes the published literature on subsurface airflow driven by natural forcings such as atmospheric pressure fluctuations, topographic effect, water table fluctuations, and water infiltration. The present state of knowledge concerning the mechanisms, analytical and numerical models, and environmental and engineering applications related to the naturally occurring airflow is discussed. Airflow induced by atmospheric pressure fluctuations is studied the most because of the applications to environmental remediation and transport of trace gases from soil to atmosphere, which are very important in understanding biogeochemical cycling and global change. Airflow induced by infiltration is also an extensively investigated topic because of its implications in rainfall infiltration and groundwater recharge. Airflow induced by water table fluctuations is important in coastal areas because it plays an important role in coastal environmental remediation and ecological systems. Airflow induced by topographic effect is studied the least. However, it has important applications in unsaturated zone gas transport and natural ventilation of mines and tunnels. Finally, the similarities and differences in the characteristics of the air pressure and airflow are compared and future research efforts are recommended.published_or_final_versio
Geomorphic signatures on Brutsaert base flow recession analysis

This paper addresses the signatures of catchment geomorphology on base flow recession curves. Its relevance relates to the implied predictability of base flow features, which are central to catchment-scale transport processes and to ecohydrological function. Moving from the classical recession curve analysis method, originally applied in the Finger Lakes Region of New York, a large set of recession curves has been analyzed from Swiss streamflow data. For these catchments, digital elevation models have been precisely analyzed and a method aimed at the geomorphic origins of recession curves has been applied to the Swiss data set. The method links river network morphology, epitomized by time-varying distribution of contributing channel sites, with the classic parameterization of recession events. This is done by assimilating two scaling exponents, β and bG, with |dQ/dt| â̂ Q β where Q is at-a-station gauged flow rate and N(l) â̂ N(l)â̂G(l)bG where l is the downstream distance from the channel heads receding in time, N(l) is the number of draining channel reaches located at distance l from their heads, and G(l) is the total drainage network length at a distance greater or equal to l, the active drainage network. We find that the method provides good results in catchments where drainage density can be regarded as spatially constant. A correction to the method is proposed which accounts for arbitrary local drainage densities affecting the local drainage inflow per unit channel length. Such corrections properly vanish when the drainage density become spatially constant. Overall, definite geomorphic signatures are recognizable for recession curves, with notable theoretical and practical implications. Key Points signatures of catchment geomorphology on base flow recession curves Analysis of streamflow data and DEM for 27 catchments in Switzerland New conceptual model accounting for uneven drainage densit
Variational Downscaling, Fusion and Assimilation of Hydrometeorological
  States via Regularized Estimation

Improved estimation of hydrometeorological states from down-sampled
observations and background model forecasts in a noisy environment, has been a
subject of growing research in the past decades. Here, we introduce a unified
framework that ties together the problems of downscaling, data fusion and data
assimilation as ill-posed inverse problems. This framework seeks solutions
beyond the classic least squares estimation paradigms by imposing proper
regularization, which are constraints consistent with the degree of smoothness
and probabilistic structure of the underlying state. We review relevant
regularization methods in derivative space and extend classic formulations of
the aforementioned problems with particular emphasis on hydrologic and
atmospheric applications. Informed by the statistical characteristics of the
state variable of interest, the central results of the paper suggest that
proper regularization can lead to a more accurate and stable recovery of the
true state and hence more skillful forecasts. In particular, using the Tikhonov
and Huber regularization in the derivative space, the promise of the proposed
framework is demonstrated in static downscaling and fusion of synthetic
multi-sensor precipitation data, while a data assimilation numerical experiment
is presented using the heat equation in a variational setting
Use of color maps and wavelet coherence to discern seasonal and interannual climate influences on streamflow variability in northern catchments

The higher midlatitudes of the northern hemisphere are particularly sensitive to change due to the important role the 0℃ isotherm plays in the phase of precipitation and intermediate storage as snow. An international intercatchment comparison program called North-Watch seeks to improve our understanding of the sensitivity of northern catchments to change by examining their hydrological and biogeochemical variability and response. Here eight North-Watch catchments located in Sweden (Krycklan), Scotland (Girnock and Strontian), the United States (Sleepers River, Hubbard Brook, and HJ Andrews), and Canada (Dorset and Wolf Creek) with 10 continuous years of daily precipitation and runoff data were selected to assess daily to seasonal coupling of precipitation (P) and runoff (Q) using wavelet coherency, and to explore the patterns and scales of variability in streamflow using color maps. Wavelet coherency revealed that P and Q were decoupled in catchments with cold winters, yet were strongly coupled during and immediately following the spring snowmelt freshet. In all catchments, coupling at shorter time scales occurred during wet periods when the catchment was responsive and storage deficits were small. At longer time scales, coupling reflected coherence between seasonal cycles, being enhanced at sites with enhanced seasonality in P. Color maps were applied as an alternative method to identify patterns and scales of flow variability. Seasonal versus transient flow variability was identified along with the persistence of that variability on influencing the flow regime. While exploratory in nature, this intercomparison exercise highlights the importance of climate and the
Variability of moisture sources in the Mediterranean region during the period 1980-2000

In this study, seasonal and interannual variability of the main atmospheric moisture sources over eight regions in the Mediterranean basin were investigated along a 21 year period. The Lagrangian dispersion model FLEXPART, developed by Stohl and James [2004, 2005], was applied to identify the contribution of humidity to the moisture budget of each region. This methodology is used to compute budgets of evaporation minus precipitation (E-P) by calculating changes in the specific humidity along backward trajectories, for the preceding 10 day periods. The results show clear seasonal differences in the moisture sources between wet and dry seasons. The Western Mediterranean Sea is the dominant moisture source for almost all the regions in the Mediterranean basin during the wet season, while the local net evaporation dominates during the dry season. The highest interannual variability is found in contributions to the Iberian Peninsula, Italy, and the Eastern Mediterranean. It is seen that the role of teleconnections is more limited than for the precipitation recorded in the region
The 5' → 3' exoribonuclease XRN1/Pacman and its functions in cellular processes and development

XRN1 is a 5' → 3' processive exoribonuclease that degrades mRNAs after they have been decapped. It is highly conserved in all eukaryotes, including homologs in Drosophila melanogaster (Pacman), Caenorhabditis elegans (XRN1), and Saccharomyces cerevisiae (Xrn1p). As well as being a key enzyme in RNA turnover, XRN1 is involved in nonsense-mediated mRNA decay and degradation of mRNAs after they have been targeted by small interfering RNAs or microRNAs. The crystal structure of XRN1 can explain its processivity and also the selectivity of the enzyme for 5' monophosphorylated RNA. In eukaryotic cells, XRN1 is often found in particles known as processing bodies (P bodies) together with other proteins involved in the 5' → 3' degradation pathway, such as DCP2 and the helicase DHH1 (Me31B). Although XRN1 shows little specificity to particular 5' monophosphorylated RNAs in vitro, mutations in XRN1 in vivo have specific phenotypes suggesting that it specifically degrades a subset of RNAs. In Drosophila, mutations in the gene encoding the XRN1 homolog pacman result in defects in wound healing, epithelial closure and stem cell renewal in testes. We propose a model where specific mRNAs are targeted to XRN1 via specific binding of miRNAs and/or RNA-binding proteins to instability elements within the RNA. These guide the RNA to the 5' core degradation apparatus for controlled degradation
Computational analysis of noncoding RNAs

Noncoding RNAs have emerged as important key players in the cell. Understanding their surprisingly diverse range of functions is challenging for experimental and computational biology. Here, we review computational methods to analyze noncoding RNAs. The topics covered include basic and advanced techniques to predict RNA structures, annotation of noncoding RNAs in genomic data, mining RNA-seq data for novel transcripts and prediction of transcript structures, computational aspects of microRNAs, and database resources.Austrian Science Fund (Schrodinger Fellowship J2966-B12)German Research Foundation (grant WI 3628/1-1 to SW)National Institutes of Health (U.S.) (NIH award 1RC1CA147187
Specificity factors in cytoplasmic polyadenylation

Poly(A) tail elongation after export of an messenger RNA (mRNA) to the cytoplasm is called cytoplasmic polyadenylation. It was first discovered in oocytes and embryos, where it has roles in meiosis and development. In recent years, however, has been implicated in many other processes, including synaptic plasticity and mitosis. This review aims to introduce cytoplasmic polyadenylation with an emphasis on the factors and elements mediating this process for different mRNAs and in different animal species. We will discuss the RNA sequence elements mediating cytoplasmic polyadenylation in the 3′ untranslated regions of mRNAs, including the CPE, MBE, TCS, eCPE, and C-CPE. In addition to describing the role of general polyadenylation factors, we discuss the specific RNA binding protein families associated with cytoplasmic polyadenylation elements, including CPEB (CPEB1, CPEB2, CPEB3, and CPEB4), Pumilio (PUM2), Musashi (MSI1, MSI2), zygote arrest (ZAR2), ELAV like proteins (ELAVL1, HuR), poly(C) binding proteins (PCBP2, αCP2, hnRNP-E2), and Bicaudal C (BICC1). Some emerging themes in cytoplasmic polyadenylation will be highlighted. To facilitate understanding for those working in different organisms and fields, particularly those who are analyzing high throughput data, HUGO gene nomenclature for the human orthologs is used throughout. Where human orthologs have not been clearly identified, reference is made to protein families identified in man.Peer-reviewedPublisher Versio
Means to an end: mechanisms of alternative polyadenylation of messenger RNA precursors

Expression of mature messenger RNAs (mRNAs) requires appropriate transcription initiation and termination, as well as pre-mRNA processing by capping, splicing, cleavage, and polyadenylation. A core 3'-end processing complex carries out the cleavage and polyadenylation reactions, but many proteins have been implicated in the selection of polyadenylation sites among the multiple alternatives that eukaryotic genes typically have. In recent years, high-throughput approaches to map both the 3'-end processing sites as well as the binding sites of proteins that are involved in the selection of cleavage sites and in the processing reactions have been developed. Here, we review these approaches as well as the insights into the mechanisms of polyadenylation that emerged from genome-wide studies of polyadenylation across a range of cell types and states. Conflict of interest: The authors have declared no conflicts of interest for this article. For further resources related to this article, please visit the WIREs website
Splicing factor mutations and cancer.

Recent advances in high-throughput sequencing technologies have unexpectedly revealed that somatic mutations of splicing factor genes frequently occurred in several types of hematological malignancies, including myelodysplastic syndromes, other myeloid neoplasms, and chronic lymphocytic leukemia. Splicing factor mutations have also been reported in solid cancers such as breast and pancreatic cancers, uveal melanomas, and lung adenocarcinomas. These mutations were heterozygous and mainly affected U2AF1 (U2AF35), SRSF2 (SC35), SF3B1 (SF3B155 or SAP155), and ZRSR2 (URP), which are engaged in the initial steps of RNA splicing, including 3' splice-site recognition, and occur in a large mutually exclusive pattern, suggesting a common impact of these mutations on RNA splicing. In this study, splicing factor mutations in various types of cancers, their functional/biological effects, and their potential as therapeutic targets have been reviewed
Matrin3: connecting gene expression with the nuclear matrix

As indicated by its name, Matrin3 was discovered as a component of the nuclear matrix, an insoluble fibrogranular network that structurally organizes the nucleus. Matrin3 possesses both DNA and RNA binding domains and, consistent with this, has been shown to function at a number of stages in the life-cycle of mRNAs. These numerous activities indicate that Matrin3, and indeed the nuclear matrix, do not just provide a structural framework for nuclear activities, but play direct functional roles in these activities. Here we review the structure, functions, and molecular interactions of Matrin3 and of Matrin3-related proteins, and the pathologies that can arise upon mutation of Matrin3.We thank Clare Gooding and Dipen Rajgor for critical comments on the manuscript. Work in the CWJS lab on Matrin3 is funded by a grant from the Wellcome Trust (092900). JA was funded by a Boehringer Ingelheim Fonds studentship.This is the author accepted manuscript. The final version is available from Wiley via http://dx.doi.org/10.1002/wrna.133
Nonsense-mediated mRNA decay: novel mechanistic insights and biological impact

Nonsense-mediated mRNA decay (NMD) was originally coined to define a quality control mechanism that targets mRNAs with truncated open reading frames due to the presence of a premature termination codon. Meanwhile, it became clear that NMD has a much broader impact on gene expression and additional biological functions beyond quality control are continuously being discovered. We review here the current views regarding the molecular mechanisms of NMD, according to which NMD ensues on mRNAs that fail to terminate translation properly, and point out the gaps in our understanding. We further summarize the recent literature on an ever-rising spectrum of biological processes in which NMD appears to be involved, including homeostatic control of gene expression, development and differentiation, as well as viral defense
Transfer RNA-derived fragments: origins, processing, and functions

Deep sequencing approaches have revealed multiple types of small RNAs with known and unknown functions. In this review we focus on a recently identified group of smallRNAsthat are derived from transferRNAs(tRNAs), tRNAfragments (tRFs). We review the mechanism of their processing and their functions in mammalian cells, and highlight points of possible cross-talk between tRFs and the canonical small RNA pathway characterized by small interfering RNAs (siRNAs), microRNAs (miRNAs), and Piwi-interacting RNAs (piRNAs). We also propose a nomenclature that is based on their processing characteristics. ï£© 2011 John Wiley & Sons, Ltd. WIREs RNA 2011 2 853â862 DOI: 10.1002/wrna.9
Theoretical insights into bacterial chemotaxis

Research into understanding bacterial chemotactic systems has become a paradigm for Systems Biology. Experimental and theoretical researchers have worked hand‐in‐hand for over 40 years to understand the intricate behavior driving bacterial species, in particular how such small creatures, usually not more than 5 µm in length, detect and respond to small changes in their extracellular environment. In this review we highlight the importance that theoretical modeling has played in providing new insight and understanding into bacterial chemotaxis. We begin with an overview of the bacterial chemotaxis sensory response, before reviewing the role of theoretical modeling in understanding elements of the system on the single cell scale and features underpinning multiscale extensions to population models