bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Investigation of Ocean Model Uncertainties Through Ensemble Forecast Experiments in the Southwest Atlantic Ocean
Authors: Lima L. N. , Pezzi L. P. , Penny S. G. , Tanajura C. A. S. 
Published: December 2018

AbstractOcean general circulation models even with realistic behavior still incorporate large uncertainties from external forcing. This study involves the realization of ensemble experiments using a regional model configured for the Southwest Atlantic Ocean to investigate uncertainties derived from the external forcing such as the atmosphere and bathymetry. The investigation is based on perturbing atmospheric surface fluxes and bathymetry through a series of ensemble experiments. The results showed a strong influence of the South Atlantic Convergence Zone on the underlying ocean, 7 days after initialization. In this ocean region, precipitation and radiation flux perturbations notably impacted the sea surface salinity and sea surface temperature, by producing values of ensemble spread that exceeded 0.08 and 0.2 °C, respectively. Wind perturbations extended the impact on currents at surface, with the spread exceeding 0.1 m/s. The ocean responded faster to the bathymetric perturbations especially in shallow waters, where the dynamics are largely dominated by barotropic processes. Ensemble spread was the largest within the thermocline layer and in ocean frontal regions after a few months, but by this time, the impact on the modeled ocean obtained from either atmospheric or bathymetric perturbations was quite similar, with the internal dynamics dominating over time. In the vertical, the sea surface temperature exhibited high correlation with the subsurface temperature of the shallowest model levels within the mixed layer. Horizontal error correlations exhibited strong flow dependence at specific points on the Brazil and Malvinas Currents. This analysis will be the basis for future experiments using ensemble‐based data assimilation in the Southwest Atlantic Ocean.
Eddy‐Resolving In Situ Ocean Climatologies of Temperature and Salinity in the Northwest Atlantic Ocean
Authors: Seidov Dan , Mishonov Alexey , Reagan James , Parsons Rost 
Published: December 2018

AbstractCirculation patterns and thermohaline fields of the Northwest Atlantic are highly variable in space and time and are strongly impacted by various mesoscale phenomena such as quasi‐stationary frontal zones with sharp gradients, meandering jet‐like currents, vortexes, and filaments. These all contribute to building and maintaining complex large‐scale regional structures of ocean tracers, such as temperature and salinity, which persist over time periods of decades and longer. To reflect the existence of these long‐term mesoscale phenomena and diagnose their changes, a new high‐resolution in situ climatology of the Northwest Atlantic was developed. At its core, this eddy‐resolving climatology, with 1/10° horizontal resolution, reveals a cumulative effect of mesoscale dynamics within the Northwest Atlantic. Additionally, strong agreement exists between this in situ climatology and climatologies derived from high‐resolution satellite data, thus providing a validation of the presence of stochastic periodicity of ocean tracer patterns on decadal timescales. Furthermore, large and very localized multidecadal subsurface heat gains southeast of the Gulf Stream was diagnosed using this new high‐resolution regional climatology. It was demonstrated that the climatic shifts in the wind stress over the Northwest Atlantic may play a leading role in this heat accumulation due to subtropical water heaving through Ekman pumping. It is argued that uncovering many important details of long‐term ocean climate variability from in situ ocean data can only be ascertained through the use of eddy‐resolving climatologies.
Ediacaran Obduction of a Fore‐Arc Ophiolite in SW Iberia: A Turning Point in the Evolving Geodynamic Setting of Peri‐Gondwana
Authors: Díez Fernández Rubén , Jiménez‐Díaz Alberto , Arenas Ricardo , Pereira M. Francisco , Fernández‐Suárez Javier 
Published: December 2018

AbstractThe Calzadilla Ophiolite is an ensemble of mafic and ultramafic rocks that represents the transition between lower crust and upper mantle of a Cadomian (peri‐Gondwanan) fore arc. Mapping and structural analysis of the ophiolite demonstrates that it was obducted in latest Ediacaran times, because the Ediacaran‐Early Cambrian sedimentary series (Malcocinado Formation) discordantly covers it. The ophiolite and emplacement‐related structures are affected by Variscan deformation (Devonian‐Carboniferous), which includes SW verging overturned folds (D1) and thrusts (D2), upright folds (D3), extensional faults (D4), and later faults (D5). These phases of deformation are explained in the context of Variscan tectonics as the result of the progressive collision between Gondwana and Laurussia. Qualitative unstraining of Variscan deformation reveals the primary geometry of Ediacaran‐Cambrian structures and uncovers the generation of east verging thrusts as responsible for the primary obduction of the Calzadilla Ophiolite. Restoration of planar and linear structures associated with this event indicates an Ediacaran, east directed obduction of the ophiolite, that is, emplacement of the Cadomian fore arc onto inner sections of the northern margin of Gondwana. According to regional data, the obduction separates two extension‐dominated stages in the tectonic evolution of the African margin of northern Gondwana preserved in southern Europe. Preobduction extension brought about the onset and widening of fore‐arc and back‐arc basins in the external part of the continent, while postobduction extension facilitated the formation of extensional migmatitic domes, an oceanward migration of back‐arc spreading centers across peri‐Gondwana, and the eventual opening of a major basin such as the Rheic Ocean.
Understanding multiple days’ metro travel demand at aggregate level
Authors: Duan Zhengyu , Lei Zengxiang , Zhang Michael , Li Haifeng , Yang Dongyuan 
Published: December 2018

Day‐to‐day variation of travel demand has been rarely studied, due to the limitation of traditional transport data collection methods and the difficulty in high‐dimensional data processing. In this study, singular value decomposition (SVD) is used to study the day‐to‐day regularity of metro travel demand, based on four one‐month datasets from the metro networks of Shanghai and Shenzhen, China. The results show that SVD is a tool to understand the intrinsic structure of daily metro travel demand. It is found that daily metro travel demand can be decomposed into three constituents: periodic part, burst part and other part. The periodic part varies weekly and accounts for a majority of the travel demand of origin–destination matrix. The burst part exhibits short‐lived spikes, which are caused by special events or holidays. Also, other part varies randomly and only contributes a fraction of travel demand. Moreover, the periodic part corresponding to the two largest singular values is very stable in 2 months, and accounts for most of the travel demand. Finally, the burst part is used to analyse the impact of a collision accident. This work is helpful for short‐term travel demand prediction, metro operation schedule and emergency management.
Research on DC component decay time constant of 1000 kV AC filter circuit breakers in UHV converter station
Authors: Zhenqiang Li , Mian Fan , Ying He , Zhipeng Zha 
Published: December 2018

In hierarchically connected UHV DC projects, the 1000 kV AC filter sub‐bank in converter station is provided with two 500 kV circuit breakers. To determine the test DC component decay time constant when breakers break short‐circuit current, relevant DC project was modelled in electromagnetic transient program (EMTP) for calculations. It is pointed out that for UHV AC filter circuit breakers, the decay time constant of DC component of short‐circuit current should be determined solely based on the single‐phase to earth fault current. Calculations and analyses were made of the AC and DC components and the DC component decay time constant of filter single‐phase to earth fault current, and the time constant calculated was converted to the test value of breakers with rated short‐circuit breaking current of 63 kA. According to the research results, a time constant of 75 or 90 ms is recommended for the two 500 kV circuit breakers, and it is lower than 120 ms as required by the relevant standards, providing technical support for future breaker tests.
Reliability evaluation and thermal design of medium‐voltage converter for underwater long‐distance high‐voltage direct current transmission system
Authors: Ma Siyuan , Zhao Jinbo , Luo Cheng , Chen Qiong , Zha Ming , Xiong Qiaopo , Luo Zhiqing , Liu Qing , Cheng Lei , He Jie , Wang Heng 
Published: December 2018

Underwater long‐distance high‐voltage direct current transmission system can provide long‐term, reliable, and sustainable energy for ocean observatories system which has higher reliability requirement than onshore or conventional underwater equipment. As the main network point for high‐voltage direct current transmission system, medium‐voltage converter of the primary node is at the top layer of power supply chain and its reliability will directly affect the reliability of high‐voltage direct current transmission system. Based on a 2.5 kW medium‐voltage converter, this study proposes a method to evaluate the reliability of medium‐voltage converter with accuracy using the lifetime model of switch by analysis of component junction temperature providing theoretical foundation and technical guidance for medium‐voltage converter design. Owing to the high power density of medium‐voltage converter, the heat dissipation space is restricted to pressure vessel. This study proposes a thermal design method to ensure normal operation condition within appropriate temperature for medium‐voltage converter and verified using ANSYS finite element analysis software.
Combined molecular dynamics and neural network method for predicting protein antifreeze activity
Authors: Kozuch Daniel J. , Stillinger Frank H. , Debenedetti Pablo G. 
Published: December 2018

Significance
Antifreeze proteins offer a technologically underutilized approach for controlling the freezing of water, a process intrinsically important in broad areas, such as medicine, agriculture, and food engineering, among others. To harness this capability, a better understanding of the measurable properties involved and their quantitative contribution to the observed antifreeze effect is needed. Here, we present a physically motivated method for the prediction of antifreeze activity purely from simulation, opening routes for the design of computationally optimized antifreeze materials.
MTSS1/Src family kinase dysregulation underlies multiple inherited ataxias
Authors: Brown Alexander S. , Meera Pratap , Altindag Banu , Chopra Ravi , Perkins Emma M. , Paul Sharan , Scoles Daniel R. , Tarapore Eric , Magri Jessica , Huang Haoran , Jackson Mandy , Shakkottai Vikram G. , Otis Thomas S. , Pulst Stefan M. , Atwood Scott X. , Oro Anthony E. 
Published: December 2018

Significance
The Src family of nonreceptor tyrosine kinases (SFK) is essential for nervous system function and may contribute to neurodegeneration. Spinocerebellar ataxias (SCAs) are neurodegenerative diseases in which Purkinje neurons fire irregularly and degenerate leading to motor problems. We show that the SFK suppressor Missing-in-metastasis (MTSS1) is an ataxia gene that links multiple SCAs. MTSS1 loss results in increased SFK activity, degenerating Purkinje neurons with low firing rates, and cell death. Surprisingly, mouse models for three different SCAs show elevated SFK activity, with SCA1 and SCA2 models displaying dramatically reduced MTSS1 protein levels. Treatment of each SCA model with an SFK inhibitor corrects Purkinje basal firing and delays ataxia progression in MTSS1 mutants. Our results identify a common link among disparate neurodegenerative diseases.
Assessing the discrimination of the Kidney Donor Risk Index/Kidney Donor Profile Index scores for allograft failure and estimated glomerular filtration rate in Ireland’s National Kidney Transplant Programme
Authors: Sexton Donal J , O’Kelly Patrick , Kennedy Claire , Denton Mark , de Freitas Declan G , Magee Colm , O’Seaghdha Conall M , Conlon Peter J 
Published: December 2018

Abstract

Background
The Kidney Donor Risk Index (KDRI)/Kidney Donor Profile Index (KDPI) is relied upon for donor organ allocation in the USA, based on its association with graft failure in time-to-event models. However, the KDRI/KDPI has not been extensively evaluated in terms of predictive metrics for graft failure and allograft estimated glomerular filtration rate (eGFR) outside of the USA.

Methods
We performed a retrospective analysis of outcomes in the Irish National Kidney Transplant Service Registry for the years 2006–13. Associations of the KDRI/KDPI score with eGFR at various time points over the follow-up and ultimate graft failure were modelled.

Results
A total of 772 patients had complete data regarding KDRI/KDPI calculation and 148 of these allografts failed over the follow-up. The median and 25–75th centile for KDRI/KDPI was 51 (26–75). On repeated-measures analysis with linear mixed effects models, the KDRI/KDPI (fixed effect covariate) associated with eGFR over 5 years: eGFR = −0.25 (standard error 0.02; P < 0.001). The variability in eGFR mathematically accounted for by the KDRI/KDPI score was only 21%. The KDRI/KDPI score did not add significantly to graft failure prediction above donor age alone (categorized as > and <50 years of age) when assessed by the categorical net reclassification index.

Conclusions
In this cohort, while the KDRI/KDPI was predictive of eGFR over the follow-up, it did not provide additive discrimination above donor age alone in terms of graft failure prediction. Therefore it is unlikely to help inform decisions regarding kidney organ allocation in Ireland.
Proof of concept for quantitative urine NMR metabolomics pipeline for large-scale epidemiology and genetics
Authors: Tynkkynen Tuulia , Wang Qin , Ekholm Jussi , Anufrieva Olga , Ohukainen Pauli , Vepsäläinen Jouko , Männikkö Minna , Keinänen-Kiukaanniemi Sirkka , Holmes Michael V , Goodwin Matthew , Ring Susan , Chambers John C , Kooner Jaspal , Järvelin Marjo-Riitta , Kettunen Johannes , Hill Michael , Davey Smith George , Ala-Korpela Mika 
Published: December 2018

Abstract

Background
Quantitative molecular data from urine are rare in epidemiology and genetics. NMR spectroscopy could provide these data in high throughput, and it has already been applied in epidemiological settings to analyse urine samples. However, quantitative protocols for large-scale applications are not available.

Methods
We describe in detail how to prepare urine samples and perform NMR experiments to obtain quantitative metabolic information. Semi-automated quantitative line shape fitting analyses were set up for 43 metabolites and applied to data from various analytical test samples and from 1004 individuals from a population-based epidemiological cohort. Novel analyses on how urine metabolites associate with quantitative serum NMR metabolomics data (61 metabolic measures; n = 995) were performed. In addition, confirmatory genome-wide analyses of urine metabolites were conducted (n = 578). The fully automated quantitative regression-based spectral analysis is demonstrated for creatinine and glucose (n = 4548).

Results
Intra-assay metabolite variations were mostly <5%, indicating high robustness and accuracy of urine NMR spectroscopy methodology per se. Intra-individual metabolite variations were large, ranging from 6% to 194%. However, population-based inter-individual metabolite variations were even larger (from 14% to 1655%), providing a sound base for epidemiological applications. Metabolic associations between urine and serum were found to be clearly weaker than those within serum and within urine, indicating that urinary metabolomics data provide independent metabolic information. Two previous genome-wide hits for formate and 2-hydroxyisobutyrate were replicated at genome-wide significance.

Conclusion
Quantitative urine metabolomics data suggest broad novelty for systems epidemiology. A roadmap for an open access methodology is provided.
City Streets in Rural Places: Emerging Cities, Youth Cultures, and the Neoliberalization of Guatemala
Authors: Way J T 
Published: December 2018

Abstract
This article traces the emergence of “agro-urban” cities in rural Guatemala from the genocide of 1981–83 to the end of the millennium, paying special attention to the multilingual Mayan highlands. It weaves together a study of changes in the political economy and the built environment with an examination of the cultural transformations associated with urbanization, ethnic politics, and youth countercultures, including an outbreak of small Maya street gangs in the highlands in the late 1990s. It argues that one of the most “rural” regions on earth became home to a new, agrarian modality of the global city as the result of a stepwise process of neoliberalization and that, as part of this process, youth street cultures moved to the fore as a site of contested cultural production. Behind this surprising urbanization and cultural cosmopolitanism was massive public investment that worked to neoliberalize military structures of counterinsurgency and change the nation’s agricultural portfolio in the midst of a war that lasted until 1996. Organizations such as the World Bank, the Inter-American Development Bank, USAID, scores of NGOs, and the United Nations all played roles in these processes, just as they promoted a burgeoning Mayan Movement and helped to foment “neoliberal multiculturalism” as the politics of race came to overshadow the politics of class. In neoliberalizing Guatemala, the globally inflected city “street,” once a territory almost exclusively restricted to the capital city, took on national dimensions. It became a national commons, a social space in which youth negotiated the terms of their belonging.
High diversity of Candida glabrata in a tertiary hospital—Mwanza, Tanzania
Authors: Mushi Martha F , Gross Uwe , Mshana Stephen E , Bader Oliver 
Published: December 2018

Abstract
Candida glabrata is a genetically diverse human pathogenic yeast, whose subpopulations have been documented to vary geographically. Here, we report MLST genotypes and antifungal drug susceptibility of C. glabrata isolates from Africa. Among 47 mostly urogenital isolates, we found 13 sequence types, amounting to a 27% genetic population difference. More than half of the isolates were of novel sequence types. ST18 was most predominant and had reduced susceptibility to fluconazole. There was clear segregation of STs between urine and vaginal specimen. In Tanzania, the C. glabrata population is genetically diverse, and divergent from those seen in other countries.
Flt3 inhibition alleviates chronic kidney disease by suppressing CD103+ dendritic cell-mediated T cell activation
Authors: Wang Ruifeng , Chen Titi , Wang Chengshi , Zhang Zhiqiang , Wang Xin Maggie , Li Qing , Lee Vincent W S , Wang Yuan Min , Zheng Guoping , Alexander Stephen I , Wang Yiping , Harris David C H , Cao Qi 
Published: December 2018

AbstractBackgroundChronic kidney disease (CKD) is a global public health problem, which lacks effective treatment. Previously, we have shown that CD103+ dendritic cells (DCs) are pathogenic in adriamycin nephropathy (AN), a model of human focal segmental glomerulosclerosis (FSGS). Fms-like tyrosine kinase 3 (Flt3) is a receptor that is expressed with high specificity on tissue resident CD103+ DCs.MethodsTo test the effect on CD103+ DCs and kidney injury of inhibition of Flt3, we used a selective Flt3 inhibitor (AC220) to treat mice with AN.ResultsHuman CD141+ DCs, homologous to murine CD103+ DCs, were significantly increased in patients with FSGS. The number of kidney CD103+ DCs, but not CD103− DCs or plasmacytoid DCs, was significantly decreased in AN mice after AC220 administration. Treatment with AC220 significantly improved kidney function and reduced kidney injury and fibrosis in AN mice. AC220-treated AN mice had decreased levels of inflammatory cytokines and chemokines, tumor necrosis factor-α, interleukin (IL)-1β, IL-6, CCL2 and CCL5 and reduced kidney infiltration of CD4 T cells and CD8 T cells. The protective effect of AC220 was associated with its suppression of CD103+ DCs-mediated CD8 T cell proliferation and activation in AN mice.ConclusionFlt3 inhibitor AC220 effectively reduced kidney injury in AN mice, suggesting that this inhibitor might be a useful pharmaceutical agent to treat CKD.
Repeatable Battery for the Assessment of Neuropsychological Status (RBANS): preliminary utility in adult neuro-oncology
Authors: Loughan Ashlee R , Braun Sarah E , Lanoye Autumn 
Published: December 2018

Abstract

Background
Neurocognitive assessments have become integral to comprehensive neuro-oncology care. Existing screening tools may be insensitive to cognitive changes caused by medical treatments. Research supports the clinical value and psychometric properties of the Repeatable Battery for the Assessment of Neuropsychological Status (RBANS) in various medical populations; however, there is minimal evidence for its use in neuro-oncology. The purpose of the current study was to further explore the cognitive profile of patients with primary brain tumor (PBT) using the RBANS and to assess rates of below-expectation performance compared to normative data and estimated intellectual functioning.

Methods
Data were collected on 82 PBT patients (54% male; age range, 19-81 years). All patients were administered the RBANS-Update and the Advanced Clinical Solutions–Test of Premorbid Functioning (TOPF) according to standardized instructions. Cognitive strengths and weaknesses were identified for PBT patients. Descriptive analyses, t tests, and chi-squared tests were utilized to identify and compare cognitive profiles.

Results
Overall, cognitive performance was low average for PBT patients. When compared to standardization data, PBT patients performed significantly worse across all 5 RBANS indexes, with Attention and Memory showing the largest discrepancies. Estimated intelligence analyses reflected greater deficits in cognitive functioning than when compared to a normal distribution.

Conclusions
Preliminary research demonstrates the RBANS is an efficient screening tool to assess cognitive deficits in PBT patients. Data also support the importance of comparison to self, rather than normative distribution in ensuring proper identification and classification of patients.