bluuebunny/crossref_metadata_2025_split huggingface dataset:
Applying the hydrodynamic model to optimize the production for crystalline basement reservoir, X field, Cuu Long Basin, Vietnam
Authors: Thai Ba Ngoc , Vo Thanh Hung , Sugai Yuichi , Sasaki Kyuro , Nguele Ronald , Phi Hoang Quang Trung , Luong Bao Minh , Le Nguyen Hai Nam 
Published: August 2019

AbstractWeathered and fractured crystalline basement is known as the important unconventional reservoir in the Cuu Long Basin. Naturally fractured reservoir plays a crucial role in oil exploration to contribute for hydrocarbon production in Vietnam. However, the complexity and heterogeneity of the fractures system in the basement reservoir are challenges for oil and gas production. They require the realistic simulation scenarios to estimate the hydrocarbon potential as well as field development plan of these reservoirs. Thus, this paper aims to propose the feasibility development scenarios to improve oil recovery factor for crystalline basement reservoir, X field, Cuu Long Basin, Vietnam. First, history matching process is validated for the model to fit the actual production data (reservoir pressure, pressure, water cut in each well) in order to approach closer the fluid flow behavior through the reservoir. The manual matching was selected to adjust the actual aquifer size and permeability distribution with limit simulation runs. Next, the highest reliability matching model which approximately reflects the actual fluid flow behavior can be used as the base case to forecast the future reservoir performance through the field development plan. The most potential scenario is to add six new infill production wells, two side track wells and two water injection wells. The forecasted results indicate that this scenario yields 8% more oil recovery factor compared to the natural drive with thirteen producers. This result suggests that the precise field development plan is to increase the efficiency of the production process by increasing the displacement parameters of residual oil and reservoir sweep efficiency by stimulation. The major contribution of this paper demonstrates the merits of the field development plan in fractured basement reservoir. The findings of this study can help better understand the fluid flow behavior using the production history profiles and field development scenarios of crystalline basement reservoir of Cuu Long Basin.
Evaluating Climate Change Impacts on Soil Moisture and Groundwater Resources Within a Lake‐Affected Region
Authors: Erler Andre R. , Frey Steven K. , Khader Omar , d'Orgeville Marc , Park Young‐Jin , Hwang Hyoun‐Tae , Lapen David R. , Peltier W. Richard , Sudicky Edward A. 
Published: August 2019

AbstractThe impact of climate change on surface water resources is reasonably well studied. However, the impact on groundwater resources has only been considered by a few studies worldwide. Here we present an analysis of climate change impacts on groundwater resources in a well‐instrumented 6,800‐km2 watershed in the Laurentian Great Lakes Basin. We employ a physics‐based modeling pipeline consisting of an ensemble of high‐resolution regional climate model projections based on the Weather Research and Forecasting model and the fully integrated three‐dimensional hydrologic model HydroGeoSphere. The Weather Research and Forecasting model is run at a resolution as fine as 10 km using two different physics configurations, while HydroGeoSphere simulates the terrestrial hydrosphere at subkilometer scale, from deep groundwater to surface water, including surface water‐groundwater interactions. The two Weather Research and Forecasting model physics configurations exhibit opposite climate change responses in summer precipitation. The hydrologic simulations follow the climate forcing, but due to the memory of the subsurface, differences in summer affect the entire seasonal cycle. In the drier climate scenario groundwater levels and recharge decline, while in the wetter scenario groundwater levels rise (recharge remains unchanged). Soil moisture changes accordingly, but primarily in late summer. It is also shown that the magnitude of climate change impacts on groundwater is strongly modulated by local physiographic features. In particular, regions where the groundwater table is deep (below 2 m; 15% of the area) show a high sensitivity to changes in climate forcing. Furthermore, changes in groundwater levels, recharge, and soil moisture typically occur in the same regions, suggesting potentially compounding impacts.
Estimation of Field‐Scale Variability in Soil Saturated Hydraulic Conductivity From Rainfall‐Runoff experiments
Authors: Goyal Abhishek , Morbidelli Renato , Flammini Alessia , Corradini Corrado , Govindaraju Rao S. 
Published: August 2019

AbstractSaturated hydraulic conductivity (Ks) is among the important soil properties that influence the partitioning of rainfall into surface and subsurface waters. Point estimates of Ks are difficult to determine and exhibit large spatial variability in fields. Often, data from field‐scale rainfall‐runoff experiments are utilized to assess the properties of the Ks random field that are required in the use of field‐scale infiltration models. Standard methods of calibration are confounded by nonuniqueness and identifiability problems associated with experimental data. In this study, a new method that employed a field‐averaged infiltration model and Monte Carlo simulations was used to obtain the possible range of distributions of Ks that would describe experimental observations over a field for a rainfall event. A Shannon information‐theoretic approach was subsequently adopted to consolidate the ranges of Ks distributions over multiple rainfall events to yield the best range of Ks distributions. The method was applied to data from several rainfall‐runoff events observed under natural conditions over an experimental field characterized by a silty loam soil and a small surface slope. Results suggest the existence of numerous parameter combinations that could satisfy the experimental observations over a single rainfall event, and high variability of these combinations among different events, thereby providing insights regarding the identifiable space of Ks distributions from individual rainfall experiments. Validation results showed that the method provides a realistic estimate of our ability to quantify the spatial variability of Ks in natural fields from rainfall‐runoff experiments.
Quantifying Uncertainties in Snow Depth Mapping From Structure From Motion Photogrammetry in an Alpine Area
Authors: Goetz Jason , Brenning Alexander 
Published: August 2019

AbstractMapping snow conditions in alpine areas is crucial for monitoring local hydrology to support water resource management decisions. Recently, the use of structure‐from‐motion multiview stereo 3‐D reconstruction (or SFM photogrammetry) to derive high‐resolution digital elevation models (DEMs) has become popular for mapping snow depth in alpine areas. In this study, methods for communicating spatial uncertainties in snow depth calculated from SFM‐derived DEMs are presented using a case study in the French Alps. A spatially varying snow depth precision estimate was determined using an error propagation model based on the precision of the acquired SFM DEMs, which was obtained from repeated unmanned aerial vehicle flights. Spatially varying snow depth detection limits were determined using Student'stdistribution. It was found that snow depths as shallow as 1 to 5 cm could be detected with high confidence for most of the study area. Areas of high uncertainties were generally related to where the extent of the ground control coverage did not match in the snow‐on and snow‐off surveys and in areas with higher surface roughness. A map of the snow depth detection threshold was found to be useful for identifying areas with high uncertainties and potential biases in the SFM snow depths, such as errors due to changes in topography between DEM acquisition dates and poor SFM reconstruction.
Amplification of 9p24.1 in diffuse large B-cell lymphoma identifies a unique subset of cases that resemble primary mediastinal large B-cell lymphoma
Authors: Wang Yucai , Wenzl Kerstin , Manske Michelle K. , Asmann Yan W. , Sarangi Vivekananda , Greipp Patricia T. , Krull Jordan E. , Hartert Keenan , He Rong , Feldman Andrew L. , Maurer Matthew J. , Slager Susan L. , Nowakowski Grzegorz S. , Habermann Thomas M. , Witzig Thomas E. , Link Brian K. , Ansell Stephen M. , Cerhan James R. , Novak Anne J. 
Published: August 2019

AbstractCopy number alterations (CNAs) of 9p24.1 occur frequently in Hodgkin lymphoma, primary mediastinal large B-cell lymphoma (PMBCL), primary central nervous system lymphoma, and primary testicular lymphoma, resulting in overexpression of PD-L1 and sensitivity to PD-1 blockade-based immunotherapy. While 9p24.1 CNA was also reported in diffuse large B-cell lymphoma (DLBCL), little is known about its molecular or clinical significance. In this study, we analyzed the prevalence of 9p24.1 CNA in newly diagnosed DLBCL and examined its association with PD-L1, PD-L2, and JAK2 expression, clinical characteristics, and outcome. We found that 10% of DLBCL cases had CNA of 9p24.1, with 6.5% gains, and 3.5% amplifications. Only the cases with a 9p24.1 amplification had high levels of PD-L1, PD-L2, and JAK2 expression. Gains or amplifications of 9p24.1 were associated with a younger age and the ABC/non-GCB subtype. Compared with DLBCL cases without 9p24.1 CNA, the cases with a 9p24.1 amplification had a trend of better event-free survival. Furthermore, the amplification cases had a gene expression and mutation profile similar to those of PMBCL. Our data suggest that amplification of 9p24.1 identifies a unique subset of DLBCL with clinical and molecular features resembling PMBCL that may be amenable to PD-1 blockade-based immunotherapy.
Therapeutic Effect of pHLIP-mediated CEACAM6 Gene Silencing in Lung Adenocarcinoma
Authors: Son Seung-Myoung , Yun Jieun , Lee Sung-Hoon , Han Hye Sook , Lim Young Hyun , Woo Chang Gok , Lee Ho-Chang , Song Hyung Geun , Gu Young-Mi , Lee Hyun-Jun , Lee Ok-Jun 
Published: September 2019

AbstractCarcinoembryonic antigen-related cell adhesion molecule 6 (CEACAM6) plays an important role in lung cancer progression. Here, we examined the therapeutic efficacy of CEACAM6 gene silencing using an siRNA delivery platform targeting the acidic tumour microenvironment in a lung adenocarcinoma xenograft mouse model. An siRNA delivery vector was constructed by tethering the peptide nucleic acid form of an siRNA targeting CEACAM6 (siCEACAM6) to a peptide with a low pH-induced transmembrane structure (pHLIP) to transport siRNAs across the plasma membrane. Specific binding of the pHLIP-siCEACAM6 conjugate to A549 lung adenocarcinoma cells at low pH was demonstrated by flow cytometry. A549 cells incubated with pHLIP-siCEACAM6 at an acidic pH showed downregulated expression of endogenous CEACAM6 protein and reduced cell viability. The in vivo tumour-suppressing effects of pHLIP-siCEACAM6 in lung adenocarcinoma were assessed in a xenograft model generated by injecting BALB/c nude mice with A549 cells. pHLIP-siCEACAM6 treatment alone resulted in tumour growth inhibition of up to 35.5%. When combined with cisplatin treatment, pHLIP-siCEACAM6 markedly enhanced tumour growth inhibition by up to 47%. In conclusion, the delivery of siCEACAM6 to lung adenocarcinoma using the pHLIP peptide has therapeutic potential as a unique cancer treatment approach.
Design considerations, modelling, and control of dual‐active full bridge for electric vehicles charging applications
Authors: Jarraya Fatma , Khan Ahmad , Gastli Adel , Ben‐Brahim Lazhar , Hamila Ridha 
Published: August 2019

The dual active full bridge (DAFB) is one of the promising isolated DC/DC converter topologies that will play a significant role in the future of electric vehicle (EV) integration in smart grids (SGs). This is due to its inherent soft switching and control simplicity. Therefore, this study presents first the latest developments related to the design of DAFB converter in EV charging technology. It provides a brief discussion of the crucial recommendations regarding the reliability, efficiency, system configuration, EV charger control scheme, battery lifetime, and system materials. Then, it presents a step‐by‐step modelling approach for a non‐ideal DAFB for the purpose of designing its controller. In addition, the model provided by this study includes all non‐idealities due to the high‐frequency (HF) transformer, semiconductor switches, passive components, and digital system delays. Eventually, the proposed system design and analysis was validated by implementing a 6.1 kW prototype on Simulink and Typhoon‐HIL real‐time simulator.
Polycomb proteins as organizers of 3D genome architecture in embryonic stem cells
Authors: Pachano Tomas , Crispatzu Giuliano , Rada-Iglesias Alvaro 
Published: August 2019

Abstract
Polycomb group proteins (PcGs) control the epigenetic and transcriptional state of developmental genes and regulatory elements during mammalian embryogenesis. Moreover, PcGs can also contribute to 3D genome organization, adding an additional layer of complexity to their regulatory functions. Understanding the mechanistic basis and the dynamics of PcG-dependent chromatin structures will help us untangle the full complexity of PcG function during development. Since most studies concerning the 3D organization of PcG-bound chromatin in mammals have been performed in embryonic stem cells (ESCs), here we will focus on this cell type characterized by its unique self-renewal and pluripotency properties. More specifically, we will highlight recent findings and discuss open questions regarding how PcG-dependent changes in 3D chromatin architecture control gene expression, cellular identity and differentiation potential in ESCs. We believe that this can serve to illustrate the diverse regulatory mechanisms by which PcG proteins control the proper execution of gene expression programs during mammalian embryogenesis.
Phylogenetic tree-based microbiome association test
Authors: Kim Kang Jin , Park Jaehyun , Park Sang-Chul , Won Sungho 
Published: September 2019

Abstract

Motivation
Ecological patterns of the human microbiota exhibit high inter-subject variation, with few operational taxonomic units (OTUs) shared across individuals. To overcome these issues, non-parametric approaches, such as the Mann–Whitney U-test and Wilcoxon rank-sum test, have often been used to identify OTUs associated with host diseases. However, these approaches only use the ranks of observed relative abundances, leading to information loss, and are associated with high false-negative rates. In this study, we propose a phylogenetic tree-based microbiome association test (TMAT) to analyze the associations between microbiome OTU abundances and disease phenotypes. Phylogenetic trees illustrate patterns of similarity among different OTUs, and TMAT provides an efficient method for utilizing such information for association analyses. The proposed TMAT provides test statistics for each node, which are combined to identify mutations associated with host diseases.

Results
Power estimates of TMAT were compared with existing methods using extensive simulations based on real absolute abundances. Simulation studies showed that TMAT preserves the nominal type-1 error rate, and estimates of its statistical power generally outperformed existing methods in the considered scenarios. Furthermore, TMAT can be used to detect phylogenetic mutations associated with host diseases, providing more in-depth insight into bacterial pathology.

Availability and implementation
The 16S rRNA amplicon sequencing metagenomics datasets for colorectal carcinoma and myalgic encephalomyelitis/chronic fatigue syndrome are available from the European Nucleotide Archive (ENA) database under project accession number PRJEB6070 and PRJEB13092, respectively. TMAT was implemented in the R package. Detailed information is available at http://healthstat.snu.ac.kr/software/tmat.

Supplementary information
Supplementary data are available at Bioinformatics online.
Self-reported Neurocognitive Impairment in People Living With Human Immunodeficiency Virus (HIV): Characterizing Clusters of Patients With Similar Changes in Self-reported Neurocognitive Impairment, 2013–2017, in the Swiss HIV Cohort Study
Authors: Kusejko Katharina , Salazar-Vizcaya Luisa , Braun Dominique L , Tarr Philip E , Bernasconi Enos , Doco-Lecompte Thanh , Cavassini Matthias , Schmid Patrick , Du Pasquier Renaud , Hauser Christoph , Günthard Huldrych F , Kouyos Roger D 
Published: September 2019

AbstractBackgroundSelf-reported neurocognitive impairment (SRNI) in people living with human immunodeficiency virus type 1 (HIV-1) infection is frequent. We use longitudinal information on SRNI in the Swiss HIV Cohort Study (SHCS) to identify and characterize groups of patients with persisting SRNI over time.MethodsWe included all SHCS patients who were assessed for SRNI during at least 5 visits spanning at least 2.5 years in 2013–2017. We first compared patients with SRNI to those without SRNI over the whole study period. Second, we used a hierarchical cluster algorithm to identify groups of patients with similar changes of SRNI over time. In both analyses, we studied clinical and demographic factors potentially influencing SRNI.ResultsIn total, 79 683 questionnaires of 11 029 patients contained information about SRNI, and 8545 of 11 029 (77.5%) patients had longitudinal information. The overall percentage of patients with SRNI decreased from 19.6% in 2013 to 10.7% in 2017. Compared to patients in the cluster with low-level SRNI over time, patients in the cluster with high-level persisting SRNI more often had a prior opportunistic infection of the central nervous system (CNS) (odds ratio [OR], 3.7; P &lt; .001), imperfect adherence to antiretroviral therapy (ART) (OR, 2.8; P &lt; .001), and depression (OR, 1.9; P &lt; .001).ConclusionsAlthough overall SRNI is decreasing in the SHCS, there is a group of patients with persisting SRNI over time. Past opportunistic infections of the CNS, imperfect adherence to ART, and depression were associated most with persisting SRNI. Patients with these characteristics should be preferentially tested for neurocognitive impairment.Although overall self-reported neurocognitive impairment (SRNI) is decreasing in the Swiss HIV Cohort Study, there is a group of patients with persisting SRNI over time, characterized by more past opportunistic infections of the central nervous system, imperfect adherence to antiretroviral therapy, and depression.
Emerging Evidence for Infectious Causes of Cancer in the United States
Authors: Brown Heidi E , Dennis Leslie K , Lauro Priscilla , Jain Purva , Pelley Erin , Oren Eyal 
Published: August 2019

Abstract
Worldwide, infectious agents currently contribute to an estimated 15% of new cancer cases. Most of these (92%, or 2 million new cancer cases) are attributable to 4 infectious agents: Helicobacter pylori, human papillomavirus, and hepatitis B and C viruses. A better understanding of how infectious agents relate to the US cancer burden may assist new diagnostic and treatment efforts. We review US-specific crude mortality rates from infection-associated cancers and describe temporal and spatial trends since 1999. We review the US-specific evidence for infection-cancer associations by reporting available estimates for attributable fractions for the infection-cancer associations. Death due to cancers with established infectious associations varies geographically, but estimates for the US attributable fraction are limited to a few observational studies. To describe the burden of infection-associated cancer in the United States, additional observational studies are necessary to estimate the prevalence of infection nationally and within subpopulations. As infectious associations emerge to explain cancer etiologies, new opportunities and challenges to reducing the burden arise. Improved estimates for the United States would help target interventions to higher-risk subpopulations.
International Commissions of Inquiry in a Networked World: Unveiling the Roles of Diasporas through an Eritrean Case Study
Authors: van den Herik Larissa , van Reisen Mirjam 
Published: September 2019

Abstract
International Commissions of Inquiry (COIs) have become important components of the human rights fact-finding, accountability and transitional justice architecture. The core task of COIs is to investigate international crises and construe what happened on the ground. The increasing tendency of states under scrutiny to refuse territorial access frustrates COI performance. It leaves COIs with no option but to operate from outside the state. COIs have developed various strategies to overcome the impediment of the uncooperative state, including the use of satellite imagery, conducting extraterritorial public hearings, interviewing individuals in the territory through Skype and other media as well as collecting accounts from individuals in the diaspora. This article focuses on the engagement of COIs with the diaspora. It presents diasporas as actors that may have considerable significance for COIs in a variety of ways, beyond sharing information. The article unveils the distinct roles that diasporic actors may entertain vis-à-vis international inquiries, as subjects in need of protection, information providers, and audience and mobilization forces. Looking at the COI for Eritrea, the article tests how these different roles play out in practice and how they interrelate. It thus sheds light on the capacity of COIs to make a difference extraterritorially for individuals in the diaspora, and on the capacity of diasporic actors to influence COI findings and shape follow up. The Eritrean COI experience illustrates that a purely instrumental approach towards diasporas – one which only regards diasporas as sources of information and which fails to protect extraterritorially or tap into the greater potential of diaspora mobilization – lessens COI effectivity for broader human rights and transitional justice purposes.
Cooperative action of APJ and α1A-adrenergic receptor in vascular smooth muscle cells induces vasoconstriction
Authors: Nagano Katsumasa , Kwon Chulwon , Ishida Junji , Hashimoto Tatsuo , Kim Jun-Dal , Kishikawa Nana , Murao Mei , Kimura Kenjiro , Kasuya Yoshitoshi , Kimura Sadao , Chen Yi-Ching , Tsuchimochi Hirotsugu , Shirai Mikiyasu , Pearson James T , Fukamizu Akiyoshi 
Published: September 2019

Abstract
The apelin receptor (APJ), a receptor for apelin and elabela/apela, induces vasodilation and vasoconstriction in blood vessels. However, the prolonged effects of increased APJ-mediated signalling, involving vasoconstriction, in smooth muscle cells have not been fully characterized. Here, we investigated the vasoactive effects of APJ gain of function under the control of the smooth muscle actin (SMA) gene promoter in mice. Transgenic overexpression of APJ (SMA-APJ) conferred sensitivity to blood pressure and vascular contraction induced by apelin administration in vivo. Interestingly, ex vivo experiments showed that apelin markedly increased the vasoconstriction of isolated aorta induced by noradrenaline (NA), an agonist for α- and β-adrenergic receptors, or phenylephrine, a specific agonist for α1-adrenergic receptor (α1-AR). In addition, intracellular calcium influx was augmented by apelin with NA in HEK293T cells expressing APJ and α1A-AR. To examine the cooperative action of APJ and α1A-AR in the regulation of vasoconstriction, we developed α1A-AR deficient mice using a genome-editing technique, and then established SMA-APJ/α1A-AR-KO mice. In the latter mouse line, aortic vasoconstriction induced by a specific agonist for α1A-AR, A-61603, were significantly less than in SMA-APJ mice. These results suggest that the APJ-enhanced response requires α1A-AR to contract vessels coordinately.