bluuebunny/crossref_metadata_2025_split huggingface dataset:
Flow Regimes and Adjustment to Wind‐Driven Motions in Lake Pontchartrain Estuary: A Modeling Experiment Using FVCOM
Authors: Li Chunyan , Huang Wei , Chen Changsheng , Lin Huichan 
Published: November 2018

AbstractLake Pontchartrain is a brackish estuary and restricted lagoon in the microtidal northern Gulf of Mexico. Using a validated Finite Volume Community Ocean Model (FVCOM), we study the flow regimes and wind‐driven adjustment of circulation in this system. It is found that tidal currents are only significant in the eastern end near the open boundary. Local wind inside the estuary is important in driving the circulation including coastal currents. Numerical experiments confirm that the subtidal wind‐driven flow is in a quasi‐steady balance between wind stress and surface slope. Our results show that the adjustment of surface level inside the system to a sudden change in wind is a transient seiche, which dissipates within two to three cycles, each lasting ~3 hr. After the oscillations, the system reaches a new equilibrium. We show in theory that this is a damped oscillation and as wind changes, an adjustment to a new equilibrium goes much faster than a complete tidal period. This leads to the quasi steady state balance of subtidal wind‐driven flows with essentially no phase lag with wind even though wind changes with time continuously. Wind‐induced circulation behaves differently from the Csanady model with Earth rotation but similar to the prismatic lake model of Engelund without Coriolis: The coastal and shallow regions tend to have flows in the direction of wind, while the interior and deeper waters have return flows against the wind especially in bottom layer. The surface flow may not be in the direction of wind, while the bottom usually has broad and uniform counter wind flows.
Inertia‐Gravity Waves Revealed in Radiosonde Data at Jang Bogo Station, Antarctica (74°37′S, 164°13′E): 1. Characteristics, Energy, and Momentum Flux
Authors: Yoo J.‐H. , Choi T. , Chun H.‐Y. , Kim Y.‐H. , Song I.‐S. , Song B.‐G. 
Published: November 2018

AbstractCharacteristics of inertia‐gravity waves (IGWs) at high latitude in Antarctica are investigated using radiosondes launched daily at Jang Bogo Station (74°37′S, 164°13′E), a new Antarctic station that has been operating since 2014, in the troposphere (z = 2–7 km) and lower stratosphere (z = 15–22 km) for 25 months (December 2014 to December 2016). The vertical propagation of IGWs exhibits strong seasonal variations in the stratosphere, with an enhancement (reduction) in downward (upward)‐propagating IGWs from May to mid‐October. In the troposphere, both upward‐ and downward‐propagating IGWs have similar occurrence rates without seasonal variations. The intrinsic phase velocity of IGWs mostly direct to the west (isotropic), while the ground‐relative phase and group velocities are dominant in the east and southeast (northeast), respectively, in the stratosphere (troposphere). The intrinsic frequency, vertical wavelength, and horizontal wavelength of IGWs averaged in the troposphere (stratosphere) are 3.57f (1.93f; where f is the Coriolis parameter), 1.48 (1.48) km, and 63.06 (221.81) km, respectively. The wave energy in the stratosphere has clear seasonal variations with large values in autumn and spring, while that in the troposphere is smaller without obvious seasonal variations. Zonal and meridional momentum fluxes averaged in the stratosphere (troposphere) are −0.008 (−0.0018) and −0.0005 (0.001) m2/s2, respectively. The momentum flux of downward‐propagating IGWs in the stratosphere is mostly positive in both zonal and meridional directions, whereas the directional preference is not obvious in the troposphere. In Part 2, sources of the observed IGWs in the troposphere and stratosphere will be examined.
A Review of Geophysical Methods for Soil Structure Characterization
Authors: Romero‐Ruiz Alejandro , Linde Niklas , Keller Thomas , Or Dani 
Published: November 2018

AbstractThe growing interest in the maintenance of favorable soil structure is largely motivated by its central role in plant growth, soil ecological functioning, and impacts on surface water and energy fluxes. Soil structure pertains to the spatial arrangement of voids and solid constituents, their aggregation, and mechanical state. As a fragile product of soil biological activity that includes invisible ingredients (mechanical and ecological states), soil structure is difficult to define rigorously, and measurements of relevant metrics often rely on core samples or on episodic point measurements. The presence of soil structure has not yet been explicitly incorporated in climate and Earth systems models, partially due to incomplete methodological means to characterize it at relevant scales and to parameterize it in spatially extensive models. We seek to review the potential of harnessing geophysical methods to fill the scale gap in characterization of soil structure directly (via impact of soil pores, transport, and mechanical properties on geophysical signals) or indirectly by measurement of surrogate variables (wetness and rates of drainage). We review basic aspects of soil structure and challenges of characterization across spatial and temporal scales and how geophysical methods could be used for the task. Additionally, we propose the use of geophysical models, inversion techniques, and combination of geophysical methods for extracting soil structure information at previously unexplored spatial and temporal scales.
Crowdsourcing Methods for Data Collection in Geophysics: State of the Art, Issues, and Future Directions
Authors: Zheng Feifei , Tao Ruoling , Maier Holger R. , See Linda , Savic Dragan , Zhang Tuqiao , Chen Qiuwen , Assumpção Thaine H. , Yang Pan , Heidari Bardia , Rieckermann Jörg , Minsker Barbara , Bi Weiwei , Cai Ximing , Solomatine Dimitri , Popescu Ioana 
Published: November 2018

AbstractData are essential in all areas of geophysics. They are used to better understand and manage systems, either directly or via models. Given the complexity and spatiotemporal variability of geophysical systems (e.g., precipitation), a lack of sufficient data is a perennial problem, which is exacerbated by various drivers, such as climate change and urbanization. In recent years, crowdsourcing has become increasingly prominent as a means of supplementing data obtained from more traditional sources, particularly due to its relatively low implementation cost and ability to increase the spatial and/or temporal resolution of data significantly. Given the proliferation of different crowdsourcing methods in geophysics and the promise they have shown, it is timely to assess the state of the art in this field, to identify potential issues and map out a way forward. In this paper, crowdsourcing‐based data acquisition methods that have been used in seven domains of geophysics, including weather, precipitation, air pollution, geography, ecology, surface water, and natural hazard management, are discussed based on a review of 162 papers. In addition, a novel framework for categorizing these methods is introduced and applied to the methods used in the seven domains of geophysics considered in this review. This paper also features a review of 93 papers dealing with issues that are common to data acquisition methods in different domains of geophysics, including the management of crowdsourcing projects, data quality, data processing, and data privacy. In each of these areas, the current status is discussed and challenges and future directions are outlined.
A Randomized Controlled Trial of TELEmedicine for Patients with Inflammatory Bowel Disease (TELE-IBD)
Authors: Cross Raymond K. , Langenberg Patricia , Regueiro Miguel , Schwartz David A. , Tracy J. Kathleen , Collins Joseph F. , Katz Jonathan , Ghazi Leyla , Patil Seema A. , Quezada Sandra M. , Beaulieu Dawn , Horst Sara N. , Russman Katharine , Riaz Mahrukh , Jambaulikar Guruprasad , Sivasailam Barathi , Quinn Charlene C. 
Published: November 2018

INTRODUCTION:
Telemedicine has shown promise in inflammatory bowel disease (IBD). The objective of this study was to compare disease activity and quality of life (QoL) in a 1-year randomized trial of IBD patients receiving telemedicine vs. standard care.

METHODS:
Patients with worsening symptoms in the prior 2 years were eligible for randomization to telemedicine (monitoring via texts EOW or weekly) or standard care. The primary outcomes were the differences in change in disease activity and QoL between the groups; change in healthcare utilization among groups was a secondary aim.

RESULTS:
348 participants were enrolled (117 control group, 115 TELE-IBD EOW, and 116 TELE-IBD weekly). 259 (74.4%) completed the study. Age was 38.9 ± 12.3 years, 56.6% were women, 91.9% were Caucasian, 67.9% had Crohn’s disease (CD) and 42.5% had active disease at baseline. In CD, all groups experienced a decrease in disease activity (control −5.2 ± 5.0 to 3.7 ± 3.6, TELE-IBD EOW 4.7 ± 4.1 to 4.2 ± 3.9, and TELE-IBD weekly 4.2 ± 4.2 to 3.2 ± 3.4, p < 0.0001 for each of the groups) In UC, only controls had a significant decrease in disease activity (control 2.9 ± 3.1 to 1.4 ± 1.4, p = 0.01, TELE-IBD EOW 2.7 ± 3.1 to 1.7 ± 1.9, p = 0.35, and TELE-IBD Weekly 2.5 ± 2.5 to 2.0 ± 1.8, p = 0.31). QoL increased in all groups; the increase was significant only in TELE-IBD EOW (control 168.1 ± 34.0 to 179.3 ± 28.2, p = 0.06, TELE-IBD EOW 172.3 ± 33.1 to 181.5 ± 28.2, p = 0.03, and TELE-IBD Weekly 172.3 ± 34.5 to 179.2 ± 32.8, p = 0.10). Unadjusted and adjusted changes in disease activity and QoL were not significantly different among groups. Healthcare utilization increased in all groups. TELE-IBD weekly were less likely to have IBD-related hospitalizations and more likely to have non-invasive diagnostic tests and electronic encounters compared to controls; both TELE-IBD groups had decreased non-IBD related hospitalizations and increased telephone calls compared to controls.

DISCUSSION:
Disease activity and QoL, although improved in all participants, were not improved further through use of the TELE-IBD system. TELE-IBD participants experienced a decrease in hospitalizations with an associated increase in non-invasive diagnostic tests, telephone calls and electronic encounters. Research is needed to determine if TELE-IBD can be improved through patient engagement and whether it can decrease healthcare utilization by replacing standard care.
Convergence of independent DISC1 mutations on impaired neurite growth via decreased UNC5D expression
Authors: Srikanth Priya , Lagomarsino Valentina N. , Pearse Richard V. , Liao Meichen , Ghosh Sulagna , Nehme Ralda , Seyfried Nicholas , Eggan Kevin , Young-Pearse Tracy L. 
Published: November 2018

AbstractThe identification of convergent phenotypes in different models of psychiatric illness highlights robust phenotypes that are more likely to be implicated in disease pathophysiology. Here, we utilize human iPSCs harboring distinct mutations in DISC1 that have been found in families with major mental illness. One mutation was engineered to mimic the consequences on DISC1 protein of a balanced translocation linked to mental illness in a Scottish pedigree; the other mutation was identified in an American pedigree with a high incidence of mental illness. Directed differentiation of these iPSCs using NGN2 expression shows rapid conversion to a homogenous population of mature excitatory neurons. Both DISC1 mutations result in reduced DISC1 protein expression, and show subtle effects on certain presynaptic proteins. In addition, RNA sequencing and qPCR showed decreased expression of UNC5D, DPP10, PCDHA6, and ZNF506 in neurons with both DISC1 mutations. Longitudinal analysis of neurite outgrowth revealed decreased neurite outgrowth in neurons with each DISC1 mutation, which was mimicked by UNC5D knockdown and rescued by transient upregulation of endogenous UNC5D. This study shows a narrow range of convergent phenotypes of two mutations found in families with major mental illness, and implicates dysregulated netrin signaling in DISC1 biology.
Bortezomib, lenalidomide, and dexamethasone (VRd) followed by autologous stem cell transplant for multiple myeloma
Authors: Sidiqi M. Hasib , Aljama Mohammed A. , Bin Riaz Irbaz , Dispenzieri Angela , Muchtar Eli , Buadi Francis K. , Warsame Rahma , Lacy Martha Q. , Dingli David , Leung Nelson , Gonsalves Wilson I. , Kapoor Prashant , Kourelis Taxiarchis V. , Hogan William J. , Rajkumar S. Vincent , Kumar Shaji K. , Gertz Morie A. 
Published: November 2018

AbstractWe retrospectively reviewed all patients (n = 243) receiving bortezomib, lenalidomide, and dexamethasone (VRd) induction followed by autologous stem cell transplantation (ASCT) for multiple myeloma at the Mayo Clinic between January 2010 and April of 2017. Median age was 61 (interquartile range, 55–67) with 62% of patients being male. High-risk cytogenetic abnormalities (HRA) were present in 34% of patients. A total of 166 (68%) patients received some form of maintenance/other therapy post transplant (no maintenance (NM, n = 77), lenalidomide maintenance (LM, n = 108), bortezomib maintenance (BM, n = 39), and other therapy (OT, n = 19)). Overall response rate at day 100 post ASCT was 99% (CR 42%) with CR rate increasing to 62% at time of best response post transplant. Two year and 5 year overall survival rates were 90% and 67%, respectively, with an estimated median overall survival (OS) and progression-free survival (PFS) of 96 and 28 months, respectively. HRA was associated with a worse OS but not PFS (median OS: not reached for standard risk vs 60 months for HRA, P = 0.0006; median PFS: 27 months for standard risk vs 22 months for HRA, P = 0.70). The combination of VRd followed by ASCT is a highly effective regimen producing deep and durable responses in many patients.
Novel pleiotropic risk loci for melanoma and nevus density implicate multiple biological pathways
Authors: Duffy David L. , Zhu Gu , Li Xin , Sanna Marianna , Iles Mark M. , Jacobs Leonie C. , Evans David M. , Yazar Seyhan , Beesley Jonathan , Law Matthew H. , Kraft Peter , Visconti Alessia , Taylor John C. , Liu Fan , Wright Margaret J. , Henders Anjali K. , Bowdler Lisa , Glass Dan , Ikram M. Arfan , Uitterlinden André G. , Madden Pamela A. , Heath Andrew C. , Nelson Elliot C. , Green Adele C. , Chanock Stephen , Barrett Jennifer H. , Brown Matthew A. , Hayward Nicholas K. , MacGregor Stuart , Sturm Richard A. , Hewitt Alex W. ,   Melanoma GWAS Consortium, Lee Jeffrey E. , Brossard Myriam , Moses Eric K. , Song Fengju , Kumar Rajiv , Easton Douglas F. , Pharoah Paul D. P. , Swerdlow Anthony J. , Kypreou Katerina P. , Harland Mark , Randerson-Moor Juliette , Akslen Lars A. , Andresen Per A. , Avril Marie-Françoise , Azizi Esther , Scarrà Giovanna Bianchi , Brown Kevin M. , Dębniak Tadeusz , Elder David E. , Fang Shenying , Friedman Eitan , Galan Pilar , Ghiorzo Paola , Gillanders Elizabeth M. , Goldstein Alisa M. , Gruis Nelleke A. , Hansson Johan , Helsing Per , Hočevar Marko , Höiom Veronica , Ingvar Christian , Kanetsky Peter A. , Chen Wei V. , Landi Maria Teresa , Lang Julie , Lathrop G. Mark , Lubiński Jan , Mackie Rona M. , Mann Graham J. , Molven Anders , Novaković Srdjan , Olsson Håkan , Puig Susana , Puig-Butille Joan Anton , Radford-Smith Graham L. , van der Stoep Nienke , van Doorn Remco , Whiteman David C. , Craig Jamie E. , Schadendorf Dirk , Simms Lisa A. , Burdon Kathryn P. , Nyholt Dale R. , Pooley Karen A. , Orr Nicholas , Stratigos Alexander J. , Cust Anne E. , Ward Sarah V. , Schulze Hans-Joachim , Dunning Alison M. , Demenais Florence , Amos Christopher I. , Kayser Manfred , Hunter David J. , Newton Bishop Julia A. , Spector Timothy D. , Montgomery Grant W. , Mackey David A. , Smith George Davey , Nijsten Tamar E. , Bishop D. Timothy , Bataille Veronique , Falchi Mario , Han Jiali , Martin Nicholas G. 
Published: November 2018

AbstractThe total number of acquired melanocytic nevi on the skin is strongly correlated with melanoma risk. Here we report a meta-analysis of 11 nevus GWAS from Australia, Netherlands, UK, and USA comprising 52,506 individuals. We confirm known loci including MTAP, PLA2G6, and IRF4, and detect novel SNPs in KITLG and a region of 9q32. In a bivariate analysis combining the nevus results with a recent melanoma GWAS meta-analysis (12,874 cases, 23,203 controls), SNPs near GPRC5A, CYP1B1, PPARGC1B, HDAC4, FAM208B, DOCK8, and SYNE2 reached global significance, and other loci, including MIR146A and OBFC1, reached a suggestive level. Overall, we conclude that most nevus genes affect melanoma risk (KITLG an exception), while many melanoma risk loci do not alter nevus count. For example, variants in TERC and OBFC1 affect both traits, but other telomere length maintenance genes seem to affect melanoma risk only. Our findings implicate multiple pathways in nevogenesis.
Sustained activation of the Aryl hydrocarbon Receptor transcription factor promotes resistance to BRAF-inhibitors in melanoma
Authors: Corre Sébastien , Tardif Nina , Mouchet Nicolas , Leclair Héloïse M. , Boussemart Lise , Gautron Arthur , Bachelot Laura , Perrot Anthony , Soshilov Anatoly , Rogiers Aljosja , Rambow Florian , Dumontet Erwan , Tarte Karin , Bessede Alban , Guillemin Gilles J. , Marine Jean-Christophe , Denison Michael S. , Gilot David , Galibert Marie-Dominique 
Published: November 2018

AbstractBRAF inhibitors target the BRAF-V600E/K mutated kinase, the driver mutation found in 50% of cutaneous melanoma. They give unprecedented anti-tumor responses but acquisition of resistance ultimately limits their clinical benefit. The master regulators driving the expression of resistance-genes remain poorly understood. Here, we demonstrate that the Aryl hydrocarbon Receptor (AhR) transcription factor is constitutively activated in a subset of melanoma cells, promoting the dedifferentiation of melanoma cells and the expression of BRAFi-resistance genes. Typically, under BRAFi pressure, death of BRAFi-sensitive cells leads to an enrichment of a small subpopulation of AhR-activated and BRAFi-persister cells, responsible for relapse. Also, differentiated and BRAFi-sensitive cells can be redirected towards an AhR-dependent resistant program using AhR agonists. We thus identify Resveratrol, a clinically compatible AhR-antagonist that abrogates deleterious AhR sustained-activation. Combined with BRAFi, Resveratrol reduces the number of BRAFi-resistant cells and delays tumor growth. We thus propose AhR-impairment as a strategy to overcome melanoma resistance.
Sound identity is represented robustly in auditory cortex during perceptual constancy
Authors: Town Stephen M. , Wood Katherine C. , Bizley Jennifer K. 
Published: November 2018

AbstractPerceptual constancy requires neural representations that are selective for object identity, but also tolerant across identity-preserving transformations. How such representations arise in the brain and support perception remains unclear. Here, we study tolerant representation of sound identity in the auditory system by recording neural activity in auditory cortex of ferrets during perceptual constancy. Ferrets generalize vowel identity across variations in fundamental frequency, sound level and location, while neurons represent sound identity robustly across acoustic variations. Stimulus features are encoded with distinct time-courses in all conditions, however encoding of sound identity is delayed when animals fail to generalize and during passive listening. Neurons also encode information about task-irrelevant sound features, as well as animals’ choices and accuracy, while population decoding out-performs animals’ behavior. Our results show that during perceptual constancy, sound identity is represented robustly in auditory cortex across widely varying conditions, and behavioral generalization requires conserved timing of identity information.
MR imaging tracking of inflammation-activatable engineered neutrophils for targeted therapy of surgically treated glioma
Authors: Wu Meiying , Zhang Haixian , Tie Changjun , Yan Chunhong , Deng Zhiting , Wan Qian , Liu Xin , Yan Fei , Zheng Hairong 
Published: November 2018

AbstractCell-based drug delivery systems have shown promising capability for tumor-targeted therapy owing to the intrinsic tumor-homing and drug-carrying property of some living cells. However, imaging tracking of their migration and bio-effects is urgently needed for clinical application, especially for glioma. Here, we report the inflammation-activatable engineered neutrophils by internalizing doxorubicin-loaded magnetic mesoporous silica nanoparticles (ND-MMSNs) which can provide the potential for magnetic resonance (MR) imaging tracking of the drug-loaded cells to actively target inflamed brain tumor after surgical resection of primary tumor. The phagocytized D-MMSNs possess high drug loading efficiency and do not affect the host neutrophils’ viability, thus remarkably improving intratumoral drug concentration and delaying relapse of surgically treated glioma. Our study offers a new strategy in targeted cancer theranostics through combining the merits of living cells and nanoparticle carriers.
An E2-ubiquitin thioester-driven approach to identify substrates modified with ubiquitin and ubiquitin-like molecules
Authors: Bakos Gábor , Yu Lu , Gak Igor A. , Roumeliotis Theodoros I. , Liakopoulos Dimitris , Choudhary Jyoti S. , Mansfeld Jörg 
Published: November 2018

AbstractCovalent modifications of proteins with ubiquitin and ubiquitin-like molecules are instrumental to many biological processes. However, identifying the E3 ligase responsible for these modifications remains a major bottleneck in ubiquitin research. Here, we present an E2-thioester-driven identification (E2~dID) method for the targeted identification of substrates of specific E2 and E3 enzyme pairs. E2~dID exploits the central position of E2-conjugating enzymes in the ubiquitination cascade and provides in vitro generated biotinylated E2~ubiquitin thioester conjugates as the sole source for ubiquitination in extracts. This enables purification and mass spectrometry-based identification of modified proteins under stringent conditions independently of the biological source of the extract. We demonstrate the sensitivity and specificity of E2-dID by identifying and validating substrates of APC/C in human cells. Finally, we perform E2~dID with SUMO in S. cerevisiae, showing that this approach can be easily adapted to other ubiquitin-like modifiers and experimental models.