bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Block Model of Present‐Day Kinematics of Alaska and Western Canada
Authors: Elliott Julie , Freymueller Jeffrey T. 
Published: January 2020

AbstractWe present an updated GPS velocity field for Alaska and western Canada and use it to develop the first regionally comprehensive tectonic block model for the area based on modern geodetic data. The greatest tectonic influences along the southern margin are the translation, collision, and flat slab subduction of the Yakutat block and subduction of the Pacific plate. Northward directed velocities surrounding the Yakutat collisional front are consistent with indenter‐related deformation while southcentral Alaska is undergoing a counterclockwise rotation. Westerly velocities in western Alaska and along the Aleutian forearc suggest that crustal material is escaping into the Bering Sea region. The majority of relative plate motion is taken up along major boundary faults, but right‐lateral strike‐slip faults in interior and western Alaska accommodate part of the motion. Escape tectonics in western Alaska extends as far north as the Kaltag fault. We observe significant motion relative to North America in every part of Alaska, including the North Slope. Evidence of localized right‐lateral shear between the Totschunda and Fairweather faults suggests that strain transfer into interior Alaska has moved away from the eastern Denali‐Chatham Strait system to a more direct corridor. Observed deformation in southcentral Alaska indicates that locked portions of the Yakutat flat slab extend further east and north than previously estimated.
Data Assimilation for Climate Research: Model Parameter Estimation of Large‐Scale Condensation Scheme
Authors: Kotsuki Shunji , Sato Yousuke , Miyoshi Takemasa 
Published: January 2020

AbstractThis study proposes using data assimilation (DA) for climate research as a tool for optimizing model parameters objectively. Mitigating radiation bias is very important for climate change assessments with general circulation models. With the Nonhydrostatic ICosahedral Atmospheric Model (NICAM), this study estimated an autoconversion parameter in a large‐scale condensation scheme. We investigated two approaches to reducing radiation bias: examining useful satellite observations for parameter estimation and exploring the advantages of estimating spatially varying parameters. The parameter estimation accelerated autoconversion speed when we used liquid water path, outgoing longwave radiation, or outgoing shortwave radiation (OSR). Accelerated autoconversion reduced clouds and mitigated overestimated OSR bias of the NICAM. An ensemble‐based DA with horizontal localization can estimate spatially varying parameters. When liquid water path was used, the local parameter estimation resulted in better cloud representations and improved OSR bias in regions where shallow clouds are dominant.
Practical and Intrinsic Predictability of a Warm‐Sector Torrential Rainfall Event in the South China Monsoon Region
Authors: Wu Naigeng , Zhuang Xiaoran , Min Jinzhong , Meng Zhiyong 
Published: January 2020

AbstractWarm‐sector torrential rainfall (WR) in the South China monsoon region has long been a forecasting challenge because of the limited capability of numerical models in heavy rainfall without strong synoptic forcing. Through convection‐allowing ensemble forecasts, this study explores both the intrinsic and practical predictability of a coastal WR event on 19–20 May 2015 during SCMREX (the Southern China Monsoon Rainfall Experiment). The results show a large variability in forecast performance among different members, indicating the practical limit of predictability. In general, GOOD members tend to have a stronger low‐level southerly wind over the sea (monsoon flow) and a considerable surface cooling over the northern mountains (associated with land/mountain breeze). Further investigation via ensemble‐based sensitivity analysis shows that the occurrence of WR is closely related to the nighttime strengthened (cooling) southerly wind (temperatures) over the sea (mountains), 1–3 hr prior to the convection initiation. In contrast, spatial scaling of the initial perturbations has little impact on the forecast after 3 hr and the meso‐γ‐scale rainfall is fully decorrelated after 12 hr, suggesting an intrinsic predictability limit for lead times as short as 6–12 hr. Sensitivity experiments are conducted with the initial‐condition differences reduced by almost an order of magnitude smaller than typical ensemble perturbations, with the results demonstrating that the rainstorm might be near the point of bifurcation, where predictability is intrinsically limited. The limits of both intrinsic and practical predictability highlight the need for rapidly updated and probabilistic convection‐allowing ensemble forecasts for events of this type.
Ionospheric Tilt Measurements: Application to Traveling Ionospheric Disturbances Climatology Study
Authors: Paznukhov Vadym , Altadill David , Juan José Miguel , Blanch Estefania 
Published: January 2020

AbstractIonospheric tilt is a concept used to characterize local horizontal electron density gradients in the ionosphere using a mirror reflection model. Experimental results are presented that illustrate the validity and accuracy of such approach. Analysis of the tilt measurements collected in 2012–2014 with a digisonde at Ebro observatory (40.8°N, 0.5°E) is presented. Digisonde systems allow measuring angles of arrival of ionospherically reflected radio signals, from which the ionospheric tilts are derived. The tilts are represented in terms of North‐South and East‐West components. Using several years of observations, a climatological distribution of wavelike variations in the tilt records presumed to be associated with traveling ionospheric disturbances (TIDs) is established. Most of the observed TIDs have their main periods of 30 min to 1.5 hr which is rather typical for medium‐scale TIDs. Summertime appears to have the most frequent occurrence of TIDs. There is a good agreement between the presence of TIDs and sporadic E layer occurrence, suggesting that some TIDs can be driven by instability in the electric field which is initiated via an interhemispheric link between the E and F regions of the ionosphere. Direction of disturbance propagation is also analyzed and compared to the modeled neutral wind. There are indications that during the daytime TIDs tend to propagate in the direction opposite to the background neutral wind. This suggests that daytime TIDs are produced by atmospheric gravity waves originating in the lower atmosphere and experiencing background wind filtering effect on their upward propagation.
Can Continental Models Convey Useful Seasonal Hydrologic Information at the Catchment Scale?
Authors: Crochemore L. , Ramos M.‐H. , Pechlivanidis I. G. 
Published: January 2020

AbstractThe development and availability of climate forecasting systems have allowed the implementation of seasonal hydroclimatic services at the continental scale. User guidance and quality of the forecast information are key components to ensure user engagement and service uptake, yet forecast quality depends on the hydrologic model setup. Here, we address how seasonal forecasts from continental services can be used to address user needs at the catchment scale. We compare a continentally calibrated process‐based model (E‐HYPE) and a catchment‐specific parsimonious model (GR6J) to forecast streamflow in a set of French catchments. Results show that despite expected high performance from the catchment setup against observed streamflow, the continental setup can, in some catchments, match or even outperform the catchment‐specific setup for 3‐month aggregations and threshold exceedance. Forecast systems can become comparable when looking at statistics relative to model climatology, such as anomalies, and adequate initial conditions are the main source of skill in both systems. We highlight the need for consistency in data used in modeling chains and in tailoring service outputs for use at the catchment scale. Finally, we show that the spread in internal model states varies largely between the two systems, reflecting the differences in their setups and calibration strategies, and highlighting that caution is needed before extracting hydrologic variables other than streamflow. We overall argue that continental hydroclimatic services show potential on addressing needs at the catchment scale, yet guidance is needed to extract, tailor and use the information provided.
Mutant P53 induces MELK expression by release of wild-type P53-dependent suppression of FOXM1
Authors: Bollu Lakshmi Reddy , Shepherd Jonathan , Zhao Dekuang , Ma Yanxia , Tahaney William , Speers Corey , Mazumdar Abhijit , Mills Gordon B. , Brown Powel H. 
Published: January 2020

AbstractTriple-negative breast cancer (TNBC) is the most aggressive form of breast cancer, and is associated with a poor prognosis due to frequent distant metastasis and lack of effective targeted therapies. Previously, we identified maternal embryonic leucine zipper kinase (MELK) to be highly expressed in TNBCs as compared with ER-positive breast cancers. Here we determined the molecular mechanism by which MELK is overexpressed in TNBCs. Analysis of publicly available data sets revealed that MELK mRNA is elevated in p53-mutant breast cancers. Consistent with this observation, MELK protein levels are higher in p53-mutant vs. p53 wild-type breast cancer cells. Furthermore, inactivation of wild-type p53, by loss or mutation of the p53 gene, increases MELK expression, whereas overexpression of wild-type p53 in p53-null cells reduces MELK promoter activity and MELK expression. We further analyzed MELK expression in breast cancer data sets and compared that with known wild-type p53 target genes. This analysis revealed that MELK expression strongly correlates with genes known to be suppressed by wild-type p53. Promoter deletion studies identified a p53-responsive region within the MELK promoter that did not map to the p53 consensus response elements, but to a region containing a FOXM1-binding site. Consistent with this result, knockdown of FOXM1 reduced MELK expression in p53-mutant TNBC cells and expression of wild-type p53 reduced FOXM1 expression. ChIP assays demonstrated that expression of wild-type p53 reduces binding of E2F1 (a critical transcription factor controlling FOXM1 expression) to the FOXM1 promoter, thereby, reducing FOXM1 expression. These results show that wild-type p53 suppresses FOXM1 expression, and thus MELK expression, through indirect mechanisms. Overall, these studies demonstrate that wild-type p53 represses MELK expression by inhibiting E2F1A-dependent transcription of FOXM1 and that mutation-driven loss of wild-type p53, which frequently occurs in TNBCs, induces MELK expression by suppressing FOXM1 expression and activity in p53-mutant breast cancers.
A simple method for detecting chaos in nature
Authors: Toker Daniel , Sommer Friedrich T. , D’Esposito Mark 
Published: January 2020

AbstractChaos, or exponential sensitivity to small perturbations, appears everywhere in nature. Moreover, chaos is predicted to play diverse functional roles in living systems. A method for detecting chaos from empirical measurements should therefore be a key component of the biologist’s toolkit. But, classic chaos-detection tools are highly sensitive to measurement noise and break down for common edge cases, making it difficult to detect chaos in domains, like biology, where measurements are noisy. However, newer tools promise to overcome these limitations. Here, we combine several such tools into an automated processing pipeline, and show that our pipeline can detect the presence (or absence) of chaos in noisy recordings, even for difficult edge cases. As a first-pass application of our pipeline, we show that heart rate variability is not chaotic as some have proposed, and instead reflects a stochastic process in both health and disease. Our tool is easy-to-use and freely available.
Attenuation of NAD[P]H:quinone oxidoreductase 1 aggravates prostate cancer and tumor cell plasticity through enhanced TGFβ signaling
Authors: Thapa Dinesh , Huang Shih-Bo , Muñoz Amanda R. , Yang Xiaoyu , Bedolla Roble G. , Hung Chia-Nung , Chen Chun-Liang , Huang Tim H.-M. , Liss Michael A. , Reddick Robert L. , Miyamoto Hiroshi , Kumar Addanki P. , Ghosh Rita 
Published: January 2020

AbstractNAD[P]H:quinone oxidoreductase 1 (NQO1) regulates cell fate decisions in response to stress. Oxidative stress supports cancer maintenance and progression. Previously we showed that knockdown of NQO1 (NQO1low) prostate cancer cells upregulate pro-inflammatory cytokines and survival under hormone-deprived conditions. Here, we tested the ability of NQO1low cells to form tumors. We found NQO1low cells form aggressive tumors compared with NQO1high cells. Biopsy specimens and circulating tumor cells showed biochemical recurrent prostate cancer was associated with low NQO1. NQO1 silencing was sufficient to induce SMAD-mediated TGFβ signaling and mesenchymal markers. TGFβ treatment decreased NQO1 levels and induced molecular changes similar to NQO1 knockdown cells. Functionally, NQO1 depletion increased migration and sensitivity to oxidative stress. Collectively, this work reveals a possible new gatekeeper role for NQO1 in counteracting cellular plasticity in prostate cancer cells. Further, combining NQO1 with TGFβ signaling molecules may serve as a better signature to predict biochemical recurrence.
Cooperation of SRPK2, Numb and p53 in the malignant biology and chemosensitivity of colorectal cancer
Authors: Wang Guosen , Sheng Weiwei , Tang Jingtong , Li Xin , Zhou Jianping , Dong Ming 
Published: January 2020

Abstract
Serine-arginine protein kinase 2 (SRPK2) is aberrantly expressed in human malignancies including colorectal cancer (CRC). However, little is known about the molecular mechanisms, and the role of SRPK2 in chemosensitivity remains unexplored in CRC. We recently showed that SRPK2 promotes pancreatic cancer progression by down-regulating Numb and p53. Therefore, we investigated the cooperation between SRPK2, Numb and p53 in the cell migration, invasion and chemosensitivity of CRC in vitro. Here, we showed that SRPK2 expression was higher in CRC tumors than in nontumor tissues. SRPK2 expression was positively associated with clinicopathological characteristics of CRC patients, including tumor differentiation, T stage, N stage and UICC stage. Additionally, SRPK2 had no association with mutant p53 (mtp53) in SW480 and SW620 cells, but negatively regulated Numb and wild-type p53 (wtp53) in response to 5-fluorouracil or cisplatin treatment in HCT116 cells. Moreover, SRPK2, Numb and p53 coimmunoprecipitated into a triple complex with or without the treatment of 5-fluorouracil in HCT116 cells, and p53 knockdown reversed the up-regulation of wtp53 induced by SRPK2 silencing with chemical agent treatment. Furthermore, overexpression of SRPK2 increased cell migration and invasion and decreased chemosensitivity to 5-fluorouracil or cisplatin in HCT116 cells. Conversely, SRPK2 silencing decreased cell migration and invasion and increased chemosensitivity to 5-fluorouracil or cisplatin, yet these effects could be reversed by p53 knockdown under chemical agent treatment. These results thus reveal a novel role of SRPK2-Numb-p53 signaling in the progression of CRC and demonstrate that SRPK2 is a potential therapeutic target for CRC clinical therapy.
Management of Spontaneous Pneumothorax in Children: A Systematic Review and Meta-Analysis
Authors: Miscia Maria Enrica , Lauriti Giuseppe , Lisi Gabriele , Riccio Angela , Lelli Chiesa Pierluigi 
Published: January 2020

Abstract
Introduction Management of primary spontaneous pneumothorax (PSP) is mainly based on adults. Data are controversial with regards to its management in children. We aimed to assess: (1) the length of hospital stay (LOS) between conservative management (i.e., observation with O2 administration), aspiration/chest drain, and surgical management; (2) the risk of recurrence after nonsurgical treatment versus surgery; (3) the risk of recurrence in the presence of bullae.
Materials and Methods Using a defined search strategy, three independent investigators identified all the studies on the management of PSP in children. Case reports, opinion articles, and gray literature publications were excluded. The study was conducted according to the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines. A meta-analysis was performed using RevMan 5.3. Data are expressed as mean ± SD.
Results Of 3,089 abstracts screened, 95 full-text were analyzed, 23 were included in the quantitative analysis, and 16 were included in the meta-analysis (1,633 patients). LOS was similar between conservative and surgical management (6.2 ± 0.8 days vs. 5.9 ± 1.4 days; p = ns). Recurrence of PSP was significantly higher among children with a nonsurgical management (32%) versus those surgically treated (18%; p = 0.002). The incidence of recurrence was slightly higher in patients managed by aspiration/chest drain (34%) compared with those with a conservative management (27%; p = 0.05). Risk of recurrence in patients with or without documented bullae was not significantly different (26 vs. 38%, respectively; p = ns).
Conclusion Given the lack of a standardized management of pediatric PSP, the present study seems to demonstrate a better outcome in children treated with surgery as first-line of management.
Level of Evidence This is a Level III study.
Does Hydroxychloroquine Protect against Preeclampsia and Preterm Delivery in Systemic Lupus Erythematosus Pregnancies?
Authors: Do Samantha C. , Rizk Nada M. , Druzin Maurice L. , Simard Julia F. 
Published: January 2020

Abstract
Objective Systemic lupus erythematosus (SLE) increases the risk of complications in pregnancy. Hydroxychloroquine (HCQ) decreases flares and neonatal lupus syndrome. Limited evidence suggests that HCQ also reduces preeclampsia and preterm birth in SLE pregnancies. We studied whether HCQ was associated with lower odds of preeclampsia and preterm delivery in SLE pregnancies.
Study Design We conducted a retrospective cohort study of 129 deliveries of 110 patients with SLE delivered at a single institution (2000–2017). HCQ exposure and preeclampsia, along with other clinical data, were extracted from chart review. Crude and multivariable-adjusted logistic regression estimated odds ratios (ORs) and 95% confidence intervals (CIs).
Results A total of 41% were exposed to HCQ, of whom 13.5% were complicated by preeclampsia versus 26.3% unexposed to HCQ (adjusted OR = 0.5; 95% CI: 0.2–1.4). The difference was pronounced for first pregnancies (7 vs. 44%), but power was limited. The difference in preterm deliveries was less pronounced comparing HCQ-exposed pregnancies with HCQ-unexposed pregnancies (34 vs. 40.8%; OR = 0.3; 95% CI: 0.3–1.5).
Conclusion Pregnant SLE patients trended toward less preeclampsia and preterm delivery when treated with HCQ. Future larger studies are needed to increase the statistical power, account for additional potential confounders, and more fully account for parity.
Measurement and interpretation of Mueller matrices of barley leaves
Authors: Savenkov S.N. , Muttiah R.S. , Oberemok E.A. , Priezzhev A.V. , Kolomiets I.S. , Klimov A.S. 
Published: January 2020

Abstract
We report the results of measuring Mueller matrices for three groups of leaf samples of common barley (Hordeum vulgare): Chlorina mutant, Chlorina etiolated mutant and Cesaer varieties. The repeatability of the measurement results of Mueller matrices of such a complex and highly depolarising object as a plant leaf is demonstrated. It is shown that the barley leaves of these three groups can be reliably identified both at forward scattering and backward scattering modes; the best results are obtained in the case of forward scattering. In both cases, the most informative matrix elements are identified. It is also shown that at backward scattering mode linear dichroism comes out, the magnitude of which increases with decreasing observation angle.
Utilisation of spatial derivative measurements in circular diffuse optical tomographic imaging to improve image resolution and contrast
Authors: Lighter D. , Jiang S. , Dehghani H. 
Published: January 2020

Abstract
The resolution of images recovered using diffuse optical tomography without spatial prior information is inherently limited due to the diffusive nature of light transport in scattering dominated biological tissue. Several studies have previously reported an improvement in depth sensitivity in near infrared spectroscopy by considering the subtraction of two neighbouring measurements. A nearest neighbour, spatial derivative based algorithm is presented, in which the difference between neighbouring source-sharing source – detector pairs is considered for tomographic reconstruction. Using a circular, inward-facing optode geometry, it is shown that deeper abnormalities in oxyhaemoglobin, deoxyhaemoglobin and water can be recovered with better localisation and contrast as compared to reconstructing using absolute values of multi-wavelength data. Relative improvements of up to 25 % in quantitative accuracy of recovered physiological values are demonstrated at better resolution for cancerous tissue in a heterogeneous breast model, when using this proposed spatial derivative based parameter reconstruction.
Optical fields in porous polylactide matrices
Authors: Sviridov A.P. , Zhigarkov V.S. , Shubnyi A.G. , Yusupov V.I. 
Published: January 2020

Abstract
Optical fields induced by laser light inside porous polymer matrices (scaffolds) under stimulating effect on cells are investigated. The spectra of light scattering coefficients and anisotropy factors of porous polylactide scaffolds in the visible and near-IR ranges are determined by numerical simulation based on experimental data obtained using a double integrating sphere. Studies are conducted for dry and wet scaffolds fabricated by supercritical fluid foaming and surface-selective laser sintering. The Monte Carlo method is used to calculate the fluence rate distribution under the assumptions of the Henyey – Greenstein phase scattering function and the model phase function of scattering on spherical cavities. It is shown that th e fluence rate distribution mainly depends on the scattering coefficient and the mean cosine of the deflection angle (g-factor). The results obtained are of great practical importance for tissue engineering based on the use of polymeric porous scaffolds with cells to replace tissue defects; they can be used to determine the dose range for laser stimulation of cells.
Bile acids and ceramide overcome the entry restriction for GII.3 human norovirus replication in human intestinal enteroids
Authors: Murakami Kosuke , Tenge Victoria R. , Karandikar Umesh C. , Lin Shih-Ching , Ramani Sasirekha , Ettayebi Khalil , Crawford Sue E. , Zeng Xi-Lei , Neill Frederick H. , Ayyar B. Vijayalakshmi , Katayama Kazuhiko , Graham David Y. , Bieberich Erhard , Atmar Robert L. , Estes Mary K. 
Published: January 2020

Significance
Many viral pathogens replicate in the human small intestine where they must invade the epithelial barrier that has evolved to protect the host against microbial assaults. Using a human norovirus strain that requires bile to replicate in stem cell-derived human small intestinal enteroid cultures, we found that conjugated hydrophobic bile acids and ceramide are critical to allow virus entry and subsequent replication in jejunal enteroids. Glycochenodeoxycholic acid treatment of enteroids below the critical micellar concentration leads to multiple cellular responses, including rapid changes in endocytosis and exocytosis dynamics that the bile-requiring human norovirus deftly exploits to overcome the epithelial barrier. Our findings shed light on the role of bile acids and ceramide in human jejunal enterocytes that stimulate viral infection.