bluuebunny/crossref_metadata_2025_split huggingface dataset:
Convective‐Reactive CO2 Dissolution in Aquifers With Mass Transfer With Immobile Water
Authors: Babaei Masoud , Islam Akand 
Published: November 2018

AbstractThe objective of this paper is to study the impact of immobile water, its fraction, and its mass transfer with the flowing region on efficiency of CO2 dissolution in aquifers with an immobile water zone. A continuum scale code is developed with underlying assumptions of spatially homogeneous and temporally invariable partitioning fraction of the porous media, first‐order mass transfer between the mobile and immobile zones, and simplified reaction of CO2 aqueous solution with calcium carbonate rock. Using ranges of values for Damköhler number (Da), fraction of the total pore volume, and mass transfer coefficient rate (α), 96 simulations are conducted. It is shown that due to a lower intensity of reaction in the mobile region, intermediate values of α serve as a threshold below which the mass transfer coefficient is not affecting the overall CO2 storage and above which overall CO2 storage increases as a function of mass transfer coefficient. Additionally, we found that (i) when α is high and geochemistry is intensive (high Da), the overall CO2 storage decreases with increase in fraction of mobile water. This is because CO2 storage through consumption of rock in immobile water with higher geochemistry is reduced. (ii) When α is high but Da is low, the system is effectively a single porosity medium with no chemistry‐influenced discrimination between mobile and immobile zones, and therefore, overall CO2 storage increases with fraction of mobile water. (iii) When α is low, the magnitude of Da does not influence the overall CO2 storage.
New Semi‐Analytical Insights Into Stress‐Dependent Spontaneous Imbibition and Oil Recovery in Naturally Fractured Carbonate Reservoirs
Authors: Haghi Amir H. , Chalaturnyk Richard , Geiger Sebastian 
Published: November 2018

AbstractFluid injection and withdrawal in a porous medium create changes in pore pressure that alter effective stresses within the medium. This leads to pore volume changes, which can be described by the poroelastic theory. These changes in pore volume can influence fluid flow processes, such as capillary diffusion and imbibition, potentially altering multiphase flow characteristics in subsurface reservoirs with a focus on oil recovery in the naturally fractured carbonate reservoirs. In this study, a semi‐analytical model is developed to analyze the impact of stress‐dependent spontaneous imbibition. The model allows us to study the influence of stress‐dependent effects on porosity, absolute permeability, relative permeability, and capillary pressure on the imbibition and oil recovery mechanisms of both intact rock and fracture in naturally fractured carbonate reservoirs. In order to capture the geomechanical interactions involved, pure compliance poroelastic definitions and nonlinear joint normal stiffness equations are used to assess the deformation of intact rock and fracture, respectively. The model shows that increasing effective confining stress shifts the imbibition capillary pressure curve upward, resulting in improved absorption of the wetting phase into the smaller pores and enhanced extraction of the nonwetting phase. Model calculations provide a rationale for how and why irreducible water saturation increases during compression of mixed‐wet carbonates and decreases in the case of initially strong water‐wet carbonates. It is also shown how higher relative permeability of the wetting phase leads to a greater diffusion of the wetting phase and improved oil recovery for the less deformed mixed‐wet rock.
Promotion of tumor progression and cancer stemness by MUC15 in thyroid cancer via the GPCR/ERK and integrin-FAK signaling pathways
Authors: Choi Cheolwon , Thi Thao Tran Nguyen , Van Ngu Trinh , Park Sae Woong , Song Min Suk , Kim Sung Hyun , Bae Yun-Ui , Ayudthaya Penchatr Diskul Na , Munir Javaria , Kim Eunbit , Baek Moo-Jun , Song Sujung , Ryu Seongho , Nam Kee-Hyun 
Published: November 2018

AbstractThyroid cancer is the fifth most common cancer diagnosed in women worldwide. Notwithstanding advancements in the prognosis and treatment of thyroid cancer, 10–20% of thyroid cancer patients develops chemotherapeutic resistance and experience relapse. According to previous reports and TCGA database, MUC15 (MUCIN 15) upregulation is highly correlated with thyroid cancer progression. However, the role of MUC15 in tumor progression and metastasis is unclear. This study aimed to investigate factors mediating cancer stemness in thyroid cancer. MUC15 plays an important role in sphere formation, as an evident from the expression of stemness markers including SOX2, KLF4, ALDH1A3, and IL6. Furthermore, ectopic expression of MUC15 activated extracellular signal-regulated kinase (ERK) signaling via G-protein–coupled receptor (GPCR)/cyclic AMP (cAMP) and integrin/focal adhesion kinase pathways. Interestingly, ectopic expression of MUC15 did not affect RAF/mitogen-activated protein kinase kinase (MEK)-mediated ERK activation. The present findings may provide novel insights into the development of diagnostic, prognostic, and therapeutic applications of MUC15 in thyroid cancer.
Prognostic and therapeutic significance of phosphorylated STAT3 and protein tyrosine phosphatase-6 in peripheral-T cell lymphoma
Authors: Han Jing Jing , O’byrne Megan , Stenson Mary J. , Maurer Matthew J. , Wellik Linda E. , Feldman Andrew L. , McPhail Ellen D. , Witzig Thomas E. , Gupta Mamta 
Published: November 2018

AbstractPeripheral T cell lymphomas (PTCL) is a heterogenous group of non-Hodgkin lymphoma and many patients remain refractory to the frontline therapy. Identifying new prognostic markers and treatment is an unmet need in PTCL. We analyzed phospho-STAT3 (pSTAT3) expression in a cohort of 169 PTCL tumors and show overall 38% positivity with varied distribution among PTCL subtypes with 27% (16/59) in PTCL-NOS; 29% (11/38) in AITL, 57% (13/28) in ALK-negative ALCL, and 93% in ALK-pos ALCL (14/15), respectively. Correlative analysis indicated an adverse correlation between pSTAT3 and overall survival (OS). PTPN6, a tyrosine phosphatase and potential negative regulator of STAT3 activity, was suppressed in 62% of PTCL-NOS, 42% of AITL, 60% ALK-neg ALCL, and 86% of ALK-pos ALCL. Loss of PTPN6 combined with pSTAT3 positivity predicted an infwere considered significantferior OS in PTCL cases. In vitro treatment of TCL lines with azacytidine (aza), a DNA methyltransferase inhibitor (DNMTi), restored PTPN6 expression and decreased pSTAT3. Combining DNMTi with JAK3 inhibitor resulted in synergistic antitumor activity in SUDHL1 cell line. Overall, our results suggest that PTPN6 and activated STAT3 can be developed as prognostic markers, and the combination of DNMTi and JAK3 inhibitors as a novel treatment for patients with PTCL subtypes.
Hydroxyurea prevents arterial and late venous thrombotic recurrences in patients with myeloproliferative neoplasms but fails in the splanchnic venous district. Pooled analysis of 1500 cases
Authors: De Stefano Valerio , Rossi Elena , Carobbio Alessandra , Ghirardi Arianna , Betti Silvia , Finazzi Guido , Vannucchi Alessandro M. , Barbui Tiziano 
Published: November 2018

AbstractWe collected 1500 patients with myeloproliferative neoplasms (MPN) and arterial or venous thrombosis (935/565), pooling three independent cohorts previously reported. Long-term treatment with antiplatelet drugs or vitamin K-antagonists (VKA) was given to 1391 (92.7%) patients; 975 (65%) patients received hydroxyurea (HU). We recorded 348 recurrences (venous in 142 cases) over 6075 patient-years, with an incidence rate of 5.7 per 100 pt-years (95% CI 5.1–6.4). The site of the first thrombosis predicted the site of recurrence. Independent factors influencing the rate of novel arterial thrombosis were HU (HR 0.67, 95% CI 0.46–0.98), antiplatelet treatment (HR 0.54, 95% CI 0.35–0.82), and VKA (HR 0.58, 95% CI 0.35–0.96). On the contrary, the recurrence of venous thromboses was significantly diminished only by VKA (HR 0.60, 95% CI 0.37–0.95), while HU prevented late but not early recurrences after venous thrombosis at common sites. Of note, we failed to demonstrate a positive effect of HU in the prevention of recurrent splanchnic vein thrombosis. In conclusion, in MPN patients, HU plays a role in the prevention of arterial thrombosis, together with aspirin and VKA, whereas its action in the prevention of recurrent venous thrombosis is uncertain. Such findings call for future studies to optimize and personalize secondary prophylaxis after MPN-related thrombosis.
Brain injury induces HIF-1α-dependent transcriptional activation of LRRK2 that exacerbates brain damage
Authors: Bae Yun-Hee , Joo Hyejin , Bae Jinhyun , Hyeon Seung Jae , Her Song , Ko Eunhwa , Choi Hwan Geun , Ryu Hoon , Hur Eun-Mi , Bu Youngmin , Lee Byoung Dae 
Published: November 2018

AbstractLeucine-rich repeat kinase 2 (LRRK2), originally identified as a causative genetic factor in Parkinson’s disease, is now associated with a number of pathologies. Here, we show that brain injury induces a robust expression of endogenous LRRK2 and suggest a role of LRRK2 after injury. We found that various in vitro and in vivo models of traumatic brain injury (TBI) markedly enhanced LRRK2 expression in neurons and also increased the level of hypoxia-inducible factor (HIF)-1α. Luciferase reporter assay and chromatin immunoprecipitation revealed direct binding of HIF-1α in LRRK2 proximal promoter. We also found that HIF-1α-dependent transcriptional induction of LRRK2 exacerbated neuronal cell death following injury. Furthermore, application of G1023, a specific, brain-permeable inhibitor of LRRK2, substantially prevented brain tissue damage, cell death, and inflammatory response and alleviated motor and cognitive defects induced by controlled cortical impact injury. Together, these results suggest HIF-1α-LRRK2 axis as a potential therapeutic target for brain injury.
A delayed diagnosis of Pallister-Hall syndrome in an adult male following the incidental detection of a hypothalamic hamartoma
Authors: Courtney Eliza , Swee Du Soon , Ishak Diana , Ngeow Joanne 
Published: November 2018

AbstractPallister-Hall syndrome is a rare autosomal dominant condition that is associated with polydactyly and hypothalamic hamartoma and is caused predominantly by frameshift or nonsense pathogenic variants in the GLI3 gene. The majority of cases are identified during childhood; however, rare reports of diagnoses during adulthood exist. Here, we describe the identification of a novel nonsense GLI3 pathogenic variant in an adult male following the incidental detection of a hypothalamic hamartoma.
A majority of HIV persistence during antiretroviral therapy is due to infected cell proliferation
Authors: Reeves Daniel B. , Duke Elizabeth R. , Wagner Thor A. , Palmer Sarah E. , Spivak Adam M. , Schiffer Joshua T. 
Published: November 2018

AbstractAntiretroviral therapy (ART) suppresses viral replication in people living with HIV. Yet, infected cells persist for decades on ART and viremia returns if ART is stopped. Persistence has been attributed to viral replication in an ART sanctuary and long-lived and/or proliferating latently infected cells. Using ecological methods and existing data, we infer that >99% of infected cells are members of clonal populations after one year of ART. We reconcile our results with observations from the first months of ART, demonstrating mathematically how a fossil record of historic HIV replication permits observed viral evolution even while most new infected cells arise from proliferation. Together, our results imply cellular proliferation generates a majority of infected cells during ART. Therefore, reducing proliferation could decrease the size of the HIV reservoir and help achieve a functional cure.
Mechanism of copper-free Sonogashira reaction operates through palladium-palladium transmetallation
Authors: Gazvoda Martin , Virant Miha , Pinter Balazs , Košmrlj Janez 
Published: November 2018

AbstractThe seminal contributions by Sonogashira, Cassar and Heck in mid 1970s on Pd/Cu- and Pd-catalysed (copper-free) coupling of acetylenes with aryl or vinyl halides have evolved in myriad applications. Despite the enormous success both in academia and in industry, however, critical mechanistic questions of this cross-coupling process remain unresolved. In this study, experimental evidence and computational support is provided for the mechanism of copper-free Sonogashira cross-coupling reaction. In contrast to the consensus monometallic mechanism, the revealed pathway proceeds through a tandem Pd/Pd cycle linked via a multistep transmetallation process. This cycle is virtually identical to the Pd/Cu tandem mechanism of copper co-catalysed Sonogashira cross-couplings, but the role of CuI is played by a set of PdII species. Phosphine dissociation from the square-planar reactants to form transient three-coordinate Pd species initiates transmetallation and represents the rate-determining step of the process.
Multiple forest attributes underpin the supply of multiple ecosystem services
Authors: Felipe-Lucia María R. , Soliveres Santiago , Penone Caterina , Manning Peter , van der Plas Fons , Boch Steffen , Prati Daniel , Ammer Christian , Schall Peter , Gossner Martin M. , Bauhus Jürgen , Buscot Francois , Blaser Stefan , Blüthgen Nico , de Frutos Angel , Ehbrecht Martin , Frank Kevin , Goldmann Kezia , Hänsel Falk , Jung Kirsten , Kahl Tiemo , Nauss Thomas , Oelmann Yvonne , Pena Rodica , Polle Andrea , Renner Swen , Schloter Michael , Schöning Ingo , Schrumpf Marion , Schulze Ernst-Detlef , Solly Emily , Sorkau Elisabeth , Stempfhuber Barbara , Tschapka Marco , Weisser Wolfgang W. , Wubet Tesfaye , Fischer Markus , Allan Eric 
Published: November 2018

AbstractTrade-offs and synergies in the supply of forest ecosystem services are common but the drivers of these relationships are poorly understood. To guide management that seeks to promote multiple services, we investigated the relationships between 12 stand-level forest attributes, including structure, composition, heterogeneity and plant diversity, plus 4 environmental factors, and proxies for 14 ecosystem services in 150 temperate forest plots. Our results show that forest attributes are the best predictors of most ecosystem services and are also good predictors of several synergies and trade-offs between services. Environmental factors also play an important role, mostly in combination with forest attributes. Our study suggests that managing forests to increase structural heterogeneity, maintain large trees, and canopy gaps would promote the supply of multiple ecosystem services. These results highlight the potential for forest management to encourage multifunctional forests and suggest that a coordinated landscape-scale strategy could help to mitigate trade-offs in human-dominated landscapes.
Cellular metabolism constrains innate immune responses in early human ontogeny
Authors: Kan Bernard , Michalski Christina , Fu Helen , Au Hilda H. T. , Lee Kelsey , Marchant Elizabeth A. , Cheng Maye F. , Anderson-Baucum Emily , Aharoni-Simon Michal , Tilley Peter , Mirmira Raghavendra G. , Ross Colin J. , Luciani Dan S. , Jan Eric , Lavoie Pascal M. 
Published: November 2018

AbstractPathogen immune responses are profoundly attenuated in fetuses and premature infants, yet the mechanisms underlying this developmental immaturity remain unclear. Here we show transcriptomic, metabolic and polysome profiling and find that monocytes isolated from infants born early in gestation display perturbations in PPAR-γ-regulated metabolic pathways, limited glycolytic capacity and reduced ribosomal activity. These metabolic changes are linked to a lack of translation of most cytokines and of MALT1 signalosome genes essential to respond to the neonatal pathogenCandida. In contrast, they have little impact on house-keeping phagocytosis functions. Transcriptome analyses further indicate a role for mTOR and its putative negative regulatorDNA Damage Inducible Transcript 4-Likein regulating these metabolic constraints. Our results provide a molecular basis for the broad susceptibility to multiple pathogens in these infants, and suggest that the fetal immune system is metabolically programmed to avoid energetically costly, dispensable and potentially harmful immune responses during ontogeny.
CYP6AE gene cluster knockout in Helicoverpa armigera reveals role in detoxification of phytochemicals and insecticides
Authors: Wang Huidong , Shi Yu , Wang Lu , Liu Shuai , Wu Shuwen , Yang Yihua , Feyereisen René , Wu Yidong 
Published: November 2018

AbstractThe cotton bollwormHelicoverpa armigera, is one of the world’s major pest of agriculture, feeding on over 300 hosts in 68 plant families. Resistance cases to most insecticide classes have been reported for this insect. Management of this pest in agroecosystems relies on a better understanding of how it copes with phytochemical or synthetic toxins. We have used genome editing to knock out a cluster of nine P450 genes and show that this significantly reduces the survival rate of the insect when exposed to two classes of host plant chemicals and two classes of insecticides. Functional expression of all members of this gene cluster identified the P450 enzymes capable of metabolism of these xenobiotics. The CRISPR-Cas9-based reverse genetics approach in conjunction with in vitro metabolism can rapidly identify the contributions of insect P450s in xenobiotic detoxification and serve to identify candidate genes for insecticide resistance.
Graphene mechanical pixels for Interferometric Modulator Displays
Authors: Cartamil-Bueno Santiago J. , Davidovikj Dejan , Centeno Alba , Zurutuza Amaia , van der Zant Herre S. J. , Steeneken Peter G. , Houri Samer 
Published: November 2018

AbstractElectro-optic modulators based on micro-electromechanical systems have found success as elements for optical projectors, for simplified optical spectrometers, and as reflective-type screens that make use of light interference (Interferometric Modulator Display technology). The latter concept offers an exciting avenue for graphene nanomechanical structures to replace classical micro-electromechanical devices and bring about enhancement in performance, especially switching speed and voltage. In this work we study the optical response of electrically actuated graphene drumheads by means of spectrometric and stroboscopic experiments. The color reproducibility and speed of these membranes in producing the desired electro-optic modulation makes them suitable as pixels for high refresh rate displays. As a proof of concept, we demonstrate a Graphene Interferometric Modulator Display prototype with 5 μm-in-diameter pixels that compose a high resolution image (2500 pixels per inch)—equivalent to a 5″ display of 12K—whose color can be changed at frame rates of at least 400 Hz.
Cross-ecosystem carbon flows connecting ecosystems worldwide
Authors: Gounand Isabelle , Little Chelsea J. , Harvey Eric , Altermatt Florian 
Published: November 2018

AbstractEcosystems are widely interconnected by spatial flows of material, but the overall importance of these flows relative to local ecosystem functioning remains unclear. Here we provide a quantitative synthesis on spatial flows of carbon connecting ecosystems worldwide. Cross-ecosystem flows range over eight orders of magnitude, bringing between 10−3and 105 gC m−2 year−1to recipient ecosystems. Magnitudes are similar to local fluxes in freshwater and benthic ecosystems, but two to three orders of magnitude lower in terrestrial systems, demonstrating different dependencies on spatial flows among ecosystem types. The strong spatial couplings also indicate that ecosystems are vulnerable to alterations of cross-ecosystem flows. Thus, a reconsideration of ecosystem functioning, including a spatial perspective, is urgently needed.
Multi-color live-cell super-resolution volume imaging with multi-angle interference microscopy
Authors: Chen Youhua , Liu Wenjie , Zhang Zhimin , Zheng Cheng , Huang Yujia , Cao Ruizhi , Zhu Dazhao , Xu Liang , Zhang Meng , Zhang Yu-Hui , Fan Jiannan , Jin Luhong , Xu Yingke , Kuang Cuifang , Liu Xu 
Published: November 2018

AbstractImaging and tracking of near-surface three-dimensional volumetric nanoscale dynamic processes of live cells remains a challenging problem. In this paper, we propose a multi-color live-cell near-surface-volume super-resolution microscopy method that combines total internal reflection fluorescence structured illumination microscopy with multi-angle evanescent light illumination. We demonstrate that our approach of multi-angle interference microscopy is perfectly adapted to studying subcellular dynamics of mitochondria and microtubule architectures during cell migration.
Non-obstructive intracellular nanolasers
Authors: Fikouras Alasdair H. , Schubert Marcel , Karl Markus , Kumar Jothi D. , Powis Simon J. , Di Falco Andrea , Gather Malte C. 
Published: November 2018

AbstractMolecular dyes, plasmonic nanoparticles and colloidal quantum dots are widely used in biomedical optics. Their operation is usually governed by spontaneous processes, which results in broad spectral features and limited signal-to-noise ratio, thus restricting opportunities for spectral multiplexing and sensing. Lasers provide the ultimate spectral definition and background suppression, and their integration with cells has recently been demonstrated. However, laser size and threshold remain problematic. Here, we report on the design, high-throughput fabrication and intracellular integration of semiconductor nanodisk lasers. By exploiting the large optical gain and high refractive index of GaInP/AlGaInP quantum wells, we obtain lasers with volumes 1000-fold smaller than the eukaryotic nucleus (Vlaser < 0.1 µm3), lasing thresholds 500-fold below the pulse energies typically used in two-photon microscopy (Eth ≈ 0.13 pJ), and excellent spectral stability (<50 pm wavelength shift). Multiplexed labeling with these lasers allows cell-tracking through micro-pores, thus providing a powerful tool to study cell migration and cancer invasion.
Over 1000-fold enhancement of upconversion luminescence using water-dispersible metal-insulator-metal nanostructures
Authors: Das Ananda , Mao Chenchen , Cho Suehyun , Kim Kyoungsik , Park Wounjhang 
Published: November 2018

AbstractRare-earth activated upconversion nanoparticles (UCNPs) are receiving renewed attention for use in bioimaging due to their exceptional photostability and low cytotoxicity. Often, these nanoparticles are attached to plasmonic nanostructures to enhance their photoluminescence (PL) emission. However, current wet-chemistry techniques suffer from large inhomogeneity and thus low enhancement is achieved. In this paper, we report lithographically fabricated metal-insulator-metal (MIM) nanostructures that show over 1000-fold enhancement of their PL. We demonstrate the potential for bioimaging applications by dispersing the MIMs into water and imaging bladder cancer cells with them. To our knowledge, our results represent one and two orders of magnitude improvement, respectively, over the best lithographically fabricated structures and colloidal systems in the literature. The large enhancement will allow for bioimaging and therapeutics using lower particle densities or lower excitation power densities, thus increasing the sensitivity and efficacy of such procedures while decreasing potential side effects.
Author Correction: A sulfotransferase dosage-dependently regulates mouthpart polyphenism in the nematode Pristionchus pacificus
Authors: Bui Linh T. , Ivers Nicholas A. , Ragsdale Erik J. 
Published: November 2018

The original version of this Article contained errors in Figure 4. In panel a, the x axis labels of bars 6-11 were incorrect, as depicted in the associated Author Correction. These errors have been corrected in both the PDF and HTML versions of the Article.