bluuebunny/crossref_metadata_2025_split huggingface dataset:
Theoretical analysis of non‐Gaussian heterogeneity effects on subsurface flow and transport
Authors: Riva Monica , Guadagnini Alberto , Neuman Shlomo P. 
Published: March 2017

AbstractMuch of the stochastic groundwater literature is devoted to the analysis of flow and transport in Gaussian or multi‐Gaussian log hydraulic conductivity (or transmissivity) fields,
(x being a position vector), characterized by one or (less frequently) a multiplicity of spatial correlation scales. Yet Y and many other variables and their (spatial or temporal) increments, ΔY, are known to be generally non‐Gaussian. One common manifestation of non‐Gaussianity is that whereas frequency distributions of Y often exhibit mild peaks and light tails, those of increments
are generally symmetric with peaks that grow sharper, and tails that become heavier, as separation scale or lag between pairs of Y values decreases. A statistical model that captures these disparate, scale‐dependent distributions of Y and
in a unified and consistent manner has been recently proposed by us. This new “generalized sub‐Gaussian (GSG)” model has the form
where
is (generally, but not necessarily) a multiscale Gaussian random field and
is a nonnegative subordinator independent of G. The purpose of this paper is to explore analytically, in an elementary manner, lead‐order effects that non‐Gaussian heterogeneity described by the GSG model have on the stochastic description of flow and transport. Recognizing that perturbation expansion of hydraulic conductivity
diverges when Y is sub‐Gaussian, we render the expansion convergent by truncating Y's domain of definition. We then demonstrate theoretically and illustrate by way of numerical examples that, as the domain of truncation expands, (a) the variance of truncated Y (denoted by Yt) approaches that of Y and (b) the pdf (and thereby moments) of Yt increments approach those of Y increments and, as a consequence, the variogram of
approaches that of
. This in turn guarantees that perturbing
to second order in
(the standard deviation of Yt) yields results which approach those we obtain upon perturbing
to second order in
even as the corresponding series diverges. Our analysis is rendered mathematically tractable by considering mean‐uniform steady state flow in an unbounded, two‐dimensional domain of mildly heterogeneous Y with a single‐scale function G having an isotropic exponential covariance. Results consist of expressions for (a) lead‐order autocovariance and cross‐covariance functions of hydraulic head, velocity, and advective particle displacement and (b) analogues of preasymptotic as well as asymptotic Fickian dispersion coefficients. We compare these theoretically and graphically with corresponding expressions developed in the literature for Gaussian Y. We find the former to differ from the latter by a factor k =
(
denoting ensemble expectation) and the GSG covariance of longitudinal velocity to contain an additional nugget term depending on this same factor. In the limit as Y becomes Gaussian, k reduces to one and the nugget term drops out.
PeaksOverThreshold (POT): A methodology for automatic threshold estimation using goodness of fitp‐value
Authors: Solari Sebastián , Egüen Marta , Polo María José , Losada Miguel A. 
Published: March 2017

AbstractThreshold estimation in the Peaks Over Threshold (POT) method and the impact of the estimation method on the calculation of high return period quantiles and their uncertainty (or confidence intervals) are issues that are still unresolved. In the past, methods based on goodness of fit tests and EDF‐statistics have yielded satisfactory results, but their use has not yet been systematized. This paper proposes a methodology for automatic threshold estimation, based on the Anderson‐Darling EDF‐statistic and goodness of fit test. When combined with bootstrapping techniques, this methodology can be used to quantify both the uncertainty of threshold estimation and its impact on the uncertainty of high return period quantiles. This methodology was applied to several simulated series and to four precipitation/river flow data series. The results obtained confirmed its robustness. For the measured series, the estimated thresholds corresponded to those obtained by nonautomatic methods. Moreover, even though the uncertainty of the threshold estimation was high, this did not have a significant effect on the width of the confidence intervals of high return period quantiles.
Multiscale temporal variability and regional patterns in 555 years of conterminous U.S. streamflow
Authors: Ho Michelle , Lall Upmanu , Sun Xun , Cook Edward R. 
Published: March 2017

AbstractThe development of paleoclimate streamflow reconstructions in the conterminous United States (CONUS) has provided water resource managers with improved insights into multidecadal and centennial scale variability that cannot be reliably detected using shorter instrumental records. Paleoclimate streamflow reconstructions have largely focused on individual catchments limiting the ability to quantify variability across the CONUS. The Living Blended Drought Atlas (LBDA), a spatially and temporally complete 555 year long paleoclimate record of summer drought across the CONUS, provides an opportunity to reconstruct and characterize streamflow variability at a continental scale. We explore the validity of the first paleoreconstructions of streamflow that span the CONUS informed by the LBDA targeting a set of U.S. Geological Survey streamflow sites. The reconstructions are skillful under cross validation across most of the country, but the variance explained is generally low. Spatial and temporal structures of streamflow variability are analyzed using hierarchical clustering, principal component analysis, and wavelet analyses. Nine spatially coherent clusters are identified. The reconstructions show signals of contemporary droughts such as the Dust Bowl (1930s) and 1950s droughts. Decadal‐scale variability was detected in the late 1900s in the western U.S., however, similar modes of temporal variability were rarely present prior to the 1950s. The twentieth century featured longer wet spells and shorter dry spells compared with the preceding 450 years. Streamflows in the Pacific Northwest and Northeast are negatively correlated with the central U.S. suggesting the potential to mitigate some drought impacts by balancing economic activities and insurance pools across these regions during major droughts.
Biofuel as an Integrated Farm Drainage Management crop: A bioeconomic analysis
Authors: Levers L. R. , Schwabe K. A. 
Published: March 2017

AbstractIrrigated agricultural lands in arid regions often suffer from soil salinization and lack of drainage, which affect environmental quality and productivity. Integrated Farm Drainage Management (IFDM) systems, where drainage water generated from higher‐valued crops grown on high quality soils are used to irrigate salt‐tolerant crops grown on marginal soils, is one possible strategy for managing salinity and drainage problems. If the IFDM crop were a biofuel crop, both environmental and private benefits may be generated; however, little is known about this possibility. As such, we develop a bioeconomic programming model of irrigated agricultural production to examine the role salt‐tolerant biofuel crops might play within an IFDM system. Our results, generated by optimizing profits over land, water, and crop choice decisions subject to resource constraints, suggest that based on the private profits alone, biofuel crops can be a competitive alternative to the common practices of land retirement and nonbiofuel crop production under both low to high drainage water salinity. Yet IFDM biofuel crop production generates 30–35% fewer GHG emissions than the other strategies. The private market competitiveness coupled with the public good benefits may justify policy changes encouraging the growth of IFDM biofuel crops in arid agricultural areas globally.
Hyphenated hydrology: Interdisciplinary evolution of water resource science
Authors: McCurley Kathryn L. , Jawitz James W. 
Published: March 2017

AbstractHydrology has advanced considerably as a scientific discipline since its recognized inception in the mid‐twentieth century. Modern water resource related questions have forced adaptation from exclusively physical or engineering science viewpoints toward a deliberate interdisciplinary context. Over the past few decades, many of the eventual manifestations of this evolution were foreseen by prominent expert hydrologists. However, their narrative descriptions have lacked substantial quantification. This study addressed that gap by measuring the prevalence of and analyzing the relationships between the terms most frequently used by hydrologists to define and describe their research. We analyzed 16,591 journal article titles from 1965–2015 in Water Resources Research, through which the scientific dialogue and its time‐sensitive progression emerged. Our word frequency and term cooccurrence network results revealed the dynamic timing of the lateral movement of hydrology across multiple disciplines as well as the deepening of scientific discourse with respect to traditional hydrologic questions. The conversation among water resource scientists surrounding the hydrologic subdisciplines of catchment‐hydrology, hydro‐meteorology, socio‐hydrology, hydro‐climatology, and eco‐hydrology gained statistically significant momentum in the analyzed time period, while that of hydro‐geology and contaminant‐hydrology experienced periods of increase followed by significant decline. This study concludes that formerly exotic disciplines can potentially modify hydrology, prompting new insights and inspiring unconventional perspectives on old questions that may have otherwise become obsolete.
Chorus whistler wave source scales as determined from multipoint Van Allen Probe measurements
Authors: Agapitov O. , Blum L. W. , Mozer F. S. , Bonnell J. W. , Wygant J. 
Published: March 2017

AbstractWhistler mode chorus waves are particularly important in outer radiation belt dynamics due to their key role in controlling the acceleration and scattering of electrons over a very wide energy range. The key parameters for both nonlinear and quasi‐linear treatment of wave‐particle interactions are the temporal and spatial scales of the wave source region and coherence of the wave field perturbations. Neither the source scale nor the coherence scale is well established experimentally, mostly because of a lack of multipoint VLF waveform measurements. We present an unprecedentedly long interval of coordinated VLF waveform measurements (sampled at 16384 s−1) aboard the two Van Allen Probes spacecraft—9 h (0800–1200 UT and 1700–2200 UT) during two consecutive apogees on 15 July 2014. The spacecraft separations varied from about 100 to 5000 km (mostly radially); measurements covered an L shell range from 3 to 6; magnetic local time 0430–0900, and magnetic latitudes were ~15 and ~5° during the two orbits. Using time‐domain correlation techniques, the single chorus source spatial extent transverse to the background magnetic field has been determined to be about 550–650 km for upper band chorus waves with amplitudes less than 100 pT and up to 800 km for larger amplitude, lower band chorus waves. The ratio between wave amplitudes measured on the two spacecraft is also examined to reveal that the wave amplitude distribution within a single chorus element generation area can be well approximated by a Gaussian exp(−0.5 · r2/r02), with the characteristic scale r0 around 300 km. Waves detected by the two spacecraft were found to be coherent in phase at distances up to 400 km.
The global distribution of Earth's critical zone and its controlling factors
Authors: Xu Xianli , Liu Wen 
Published: March 2017

AbstractThe near‐surface layer of Earth which provides essential elements for supporting life is now recognized as the critical zone (CZ). This study provides the first global assessment of the CZ thickness (CZT) and its controlling factors by combining data sets of climate, vegetation height (VH), water table depth (WTD), groundwater thickness (GWT), topography, and lithologic data. The analysis shows that CZT ranges from 0.7 to 223.5 m with an average value of 36.8 m across continental areas; CZT is thickest in midlatitudes (subtropical to temperate zones). The proportion of aboveground part (VH) to CZT is 19.9 ± 16.7% (mean ±one standard deviation), while it is 80.1 ± 16.7% for the underground part (WTD + GWT). A generalized linear model shows that compound topographic index (ln(a/tan(b)), where a is the upslope contributing area and b is the slope degree of the landscape) and potential evapotranspiration are the first two major controlling factors on the variations in CZT. This study opens opportunities for further advancing CZ science by providing one of its most important properties—its thickness.
The Hfq regulon of Neisseria meningitidis
Authors: Huis in ‘t Veld Robert A. G. , Kramer Gertjan , van der Ende Arie , Speijer Dave , Pannekoek Yvonne 
Published: March 2017

The conserved RNA‐binding protein, Hfq, has multiple regulatory roles within the prokaryotic cell, including promoting stable duplex formation between small RNAs and mRNAs, and thus hfq deletion mutants have pleiotropic phenotypes. Previous proteome and transcriptome studies of Neisseria meningitidis have generated limited insight into differential gene expression due to Hfq loss. In this study, reversed‐phase liquid chromatography combined with data‐independent alternate scanning mass spectrometry (LC‐MSE) was utilized for rapid high‐resolution quantitative proteomic analysis to further elucidate the differentially expressed proteome of a meningococcal hfq deletion mutant. Whole‐cell lysates of N. meningitidis serogroup B H44/76 wild‐type (wt) and H44/76Δhfq (Δhfq) grown in liquid growth medium were subjected to tryptic digestion. The resulting peptide mixtures were separated by liquid chromatography (LC) prior to analysis by mass spectrometry (MSE). Differential expression was analyzed by Student's t‐test with control for false discovery rate (FDR). Reliable quantitation of relative expression comparing wt and Δhfq was achieved with 506 proteins (20%). Upon FDR control at q ≤ 0.05, 48 up‐ and 59 downregulated proteins were identified. From these, 81 were identified as novel Hfq‐regulated candidates, while 15 proteins were previously found by SDS/PAGE/MS and 24 with microarray analyses. Thus, using LC‐MSE we have expanded the repertoire of Hfq‐regulated proteins. In conjunction with previous studies, a comprehensive network of Hfq‐regulated proteins was constructed and differentially expressed proteins were found to be involved in a large variety of cellular processes. The results and comparisons with other gram‐negative model systems, suggest still unidentified sRNA analogs in N. meningitidis.
The neuronal and astrocytic proteinSLC38A10 transports glutamine, glutamate, and aspartate, suggesting a role in neurotransmission
Authors: Hellsten Sofie V. , Hägglund Maria G. , Eriksson Mikaela M. , Fredriksson Robert 
Published: March 2017

In brain cells, glutamine transporters are vital to monitor and control the levels of glutamate andGABA. There are 11 members of theSLC38 family of amino acid transporters of which eight have been functionally characterized. Here, we report the first histological and functional characterization of the previously orphan member,SLC38A10. We used pairwise global sequence alignments to determine the sequence identity between theSLC38 family members.SLC38A10 was found to share 20–25% transmembrane sequence identity with several family members, and was predicted to have 11 transmembrane helices.SLC38A10 immunostaining was abundant in mouse brain using a custom‐made anti‐SLC38A10 antibody and colocalization ofSLC38A10 immunoreactivity with markers for neurons and astrocytes was detected. UsingXenopus laevisoocytes overexpressingSLC38A10, we show thatSLC38A10 mediates bidirectional transport ofl‐glutamine,l‐alanine,l‐glutamate, andd‐aspartate, and efflux ofl‐serine. This profile mostly resembles system A members of theSLC38 family. In conclusion, the bidirectional transport of glutamine, glutamate, and aspartate bySLC38A10, and the immunostaining detected in neurons and astrocytes, suggest thatSLC38A10 plays a role in pathways involved in neurotransmission.
Cancer Genomics and Evolution
Authors: Hendricks William P. D. , Sekulic Aleksandar , Bryce Alan H. , Murtaza Muhammed , Ramos Pilar , Trent Jeffrey M. 
Published: March 2017

OverviewOver 100 years ago, the Nobel Prize in Physiology or Medicine was given to Paul Ehrlich for postulating that “magic bullets” could specifically target and kill cells such as cancer cells based on their unique molecular features. The completed Human Genome Project and the cancer genomics revolution have now mapped the specific genetic changes underlying unique features of many common malignancies. However, although cancer has long been recognized to be heterogeneous in its clinical presentation, course, and pathology, we now recognize that it is far more molecularly heterogeneous than anticipated and that such variability will require an individualized approach to patient care. Rather than a single magic bullet, we will need an arsenal and this arsenal will require precise delivery. While inter‐ and intratumoral genomic heterogeneity present significant challenges to cancer management and drug discovery, a number of developments foster hope for accelerated progress in the war on cancer. First, our catalog of genomic targets underlying diverse cancers is rapidly growing. Second, we are beginning to understand how diverse mutations converge on a small number of druggable pathways. Third, we continue to develop drugs and biologic agents (e.g., immune checkpoint inhibitors) that target an increasingly wide array of genomic subtypes of cancer. Finally, advances in next‐generation sequencing technologies now enable far earlier detection of disease recurrence than ever before. This chapter will focus on these developments and how their integration is aiding in the precise delivery of “magic bullets.”
MicroRNA
Expression in Cancer
Authors: Nana‐Sinkam Serge Patrick , Acunzo Mario , Croce Carlo M. 
Published: March 2017

Overview
In the last two decades, researchers have identified a novel group of noncoding RNAs (ncRNAs) classified according to their function and size. The best studied of these ncRNAs termed microRNAs (miRNAs) are short noncoding RNAs that are approximately 22 nucleotides in length and play a key role in the regulation of a large number of biological processes and diseases, including cancer. Since the initial description of an association between miRNA and cancer in 2002, miRNAs have emerged as central regulators of processes fundamental to the initiation and progression of cancer. More recently, miRNAs have been detected in bodily fluids including blood, sputum, and urine, thus making them potential noninvasive diagnostic and prognostic biomarkers of disease. The application of miRNAs in human cancer therapy has become a fascinating field of study, representing one of the newest frontiers for cancer treatment. However, our knowledge for these small molecules and their application to human cancers is still growing. In this chapter, we provide an overview of the connection between miRNAs and cancer with a focus on translation to human application.
Cancer Cell Immortality: Targeting Telomerase
Authors: Mender Ilgen , Gunnur Dikmen Zeliha , Wright Woodring E. , Shay Jerry W. 
Published: March 2017

Overview
Finding specific targeted agents for cancer therapy remains a challenge. One of the hallmarks of cancer is the limitless proliferation (immortalization) of cancer cells, which correlates with the activation of the ribonucleoprotein enzyme complex called telomerase. As 85–90% of primary human cancers express telomerase activity, while most normal cells do not, telomerase is a unique and almost universal therapeutic target for cancer. Although there have been several approaches developed for telomerase‐targeted therapies, there is still no agent that has been approved. This chapter focuses on the pros and cons of the different approaches to target telomerase and summarizes preclinical and clinical results. We will also review novel telomerase‐mediated telomere uncapping approaches that target telomerase‐expressing cancer cells, but not normal cells.
Systems Biology and Genomics
Authors: Hassan Saima , Heiser Laura M. , Gray Joe W. 
Published: March 2017

Overview
Cancers are complex, adaptive systems comprised of cancer cells, the proximal and distal cells, and soluble and insoluble proteins that influence the behavior of the cancer cells. Features pertaining to the cancer are referred to as intrinsic to the cancer and those comprising the proximal and distal microenvironments are referred to as extrinsic to the cancer. Genomics studies seek to develop comprehensive cellular and molecular profiles of cancers and cancer systems biology studies seek to develop the experimental and theoretical methods needed to understand how the components work together to determine cancer function. The overall goal of these efforts is to develop the ability to predict the behavior of cancers—including progression and response to therapy—from measurements of the intrinsic and extrinsic molecular and cellular components of the cancers. Here, we review recent progress in international efforts to measure the genomic, epigenomic, and proteomic features (aka omic features) of major tumor types. We summarize work on establishing associations between omic features and cancer behavior. Finally, we summarize the computational and experimental models that are currently being used to understand and manipulate the behavior of complex cancer systems.
Clinical Informatics
Authors: Ambinder Edward P. 
Published: March 2017

Overview
Informatics is the integration of information technology into health care. For oncology, the need to understand informatics is critical because of the need to keep up with the rapidly changing basic, translational and clinical cancer research findings, therapeutic interventions using panomic data required for precision medicine, latest practice guidelines, shifting reimbursement practices, and the dominating and at times frustrating electronic health record (EHR) that is the repository of our health data and window into the health care system. All of this must take place in a value‐enhanced practice environment that constantly measures our quality of care in a well‐coordinated system for our engaged patients who are digitally connected to multiple practices, their hospital, their smartphones and medical devices, their personal health record and multiple EHRs. Oncologists will soon have a well‐defined “Oncology Digital Health Information Technology System” that will redefine cancer research by capturing meaningful and actionable patient data in every cancer patient. They will continue to participate in the mobile computing revolution that is just beginning to have a transformative effect on all of medicine where computers will do our work, apps work with other apps and EHRs to educate us and our patients and use real electronically shareable and reusable medical data. Today, the majority of patients have their cancer care documented in EHRs. As rapid learning systems (RLSs) such as ASCO's CancerLinQ capture all this data and use Big Data analytic tools for capturing and comparing similar cancer patients as to the best treatments and outcomes, we will have real precision medicine. The evolving “Internet of Things” where medical devices and health care platforms will give us the unprecedented ability to measure in real time the health and wellness of our cancer patients undergoing chemotherapy treatments on a 24‐h basis will provide huge monetary savings for the health system, improved quality of care, and innovative medical research as cancer care develops into a RLS.