bluuebunny/crossref_metadata_2025_split huggingface dataset:
A survey of methods for revealing and overcoming weaknesses of data-driven Natural Language Understanding
Authors: Schlegel Viktor , Nenadic Goran , Batista-Navarro Riza 
Published: April 2022

AbstractRecent years have seen a growing number of publications that analyse Natural Language Understanding (NLU) datasets for superficial cues, whether they undermine the complexity of the tasks underlying those datasets and how they impact those models that are optimised and evaluated on this data. This structured survey provides an overview of the evolving research area by categorising reported weaknesses in models and datasets and the methods proposed to reveal and alleviate those weaknesses for the English language. We summarise and discuss the findings and conclude with a set of recommendations for possible future research directions. We hope that it will be a useful resource for researchers who propose new datasets to assess the suitability and quality of their data to evaluate various phenomena of interest, as well as those who propose novel NLU approaches, to further understand the implications of their improvements with respect to their model’s acquired capabilities.
3D cell morphology detection by association for embryo heart morphogenesis
Authors: Sarkar Rituparna , Darby Daniel , Meilhac Sigolène , Olivo-Marin Jean-Christophe 
Published: April 2022

Abstract
Advances in tissue engineering for cardiac regenerative medicine require cellular-level understanding of the mechanism of cardiac muscle growth during embryonic developmental stage. Computational methods to automatize cell segmentation in 3D and deliver accurate, quantitative morphology of cardiomyocytes, are imperative to provide insight into cell behavior underlying cardiac tissue growth. Detecting individual cells from volumetric images of dense tissue, poised with low signal-to-noise ratio and severe intensity in homogeneity, is a challenging task. In this article, we develop a robust segmentation tool capable of extracting cellular morphological parameters from 3D multifluorescence images of murine heart, captured via light-sheet microscopy. The proposed pipeline incorporates a neural network for 2D detection of nuclei and cell membranes. A graph-based global association employs the 2D nuclei detections to reconstruct 3D nuclei. A novel optimization embedding the network flow algorithm in an alternating direction method of multipliers is proposed to solve the global object association problem. The associated 3D nuclei serve as the initialization of an active mesh model to obtain the 3D segmentation of individual myocardial cells. The efficiency of our method over the state-of-the-art methods is observed via various qualitative and quantitative evaluation.
Numerical Insight Into Energy Partitioning During Stick‐Slip Events Based on the Framework of Rate‐and‐State Friction Law
Authors: Bai Qingsheng , Konietzky Heinz 
Published: April 2022

AbstractMany attempts have been made to investigate the energy budgets of stick‐slip events, however, the strain energy contribution is still poorly understood. We developed a discrete element method (DEM)‐based method to mimic stick‐slip events and the associated energy partitioning. We found that stress drop Δσ, breakdown energy EG, and strain energy release ΔU scale with slip δc as , , and , respectively, which is quantitatively consistent with data from manmade seismicity and natural earthquakes. We observed two different slip‐weakening behavior patterns: one without a postseismic phase (Type I) and one containing a postseismic phase (Type II). We show that ΔU contributes 20%∼90% (63% on average) and 10% ∼ 60% (38% on average) to the total energy budget for Type I and Type II events, respectively. Formations that store higher strain energy play a more vital role in the earthquake energy budget, regardless of the distance to the fault.
Mechanism for the Uplift of Gongga Shan in the Southeastern Tibetan Plateau Constrained by 3D Magnetotelluric Data
Authors: Jiang Feng , Chen Xiaobin , Unsworth Martyn J. , Cai Juntao , Han Bing , Wang Lifeng , Dong Zeyi , Cui Tengfa , Zhan Yan , Zhao Guoze , Tang Ji 
Published: April 2022

AbstractGongga Shan (GGS) is the highest mountain on the eastern margin of the Tibetan Plateau. However, the mechanism for the uplift of Gongga Shan is still unclear due to a lack of detailed geophysical studies. Inversion of an array of magnetotelluric data at 120 sites produced a 3D resistivity model that revealed that the GGS massif is characterized by a high resistivity upper crust underlain by a westward dipping resistor at middle crustal depths that is interpreted as the underthrust Yangtze Craton (YC). A thin conductive layer is sandwiched between these two zones of high resistivity. This resistivity model is inconsistent with previously published geodynamic models. Based on the new magnetotelluric results, we propose that the uplift of Gongga Shan occurs primarily by underthrusting of the YC. Additional uplift may be due to transpression on a restraining bend of the oblique‐slip Xianshuihe faults.
On the Relationship Between the Stratospheric Quasi‐Biennial Oscillation and Summer Precipitation in Northern China
Authors: Hu Jinggao , Gao Xiang , Ren Rongcai , Luo Jingjia , Deng Jiechun , Xu Haiming 
Published: April 2022

AbstractThis paper reports that there has been a significant relationship between the quasi‐biennial oscillation (QBO) in zonal wind at 50 hPa in summer and precipitation in August in northern China since the late 1970s. The correlation coefficient between them reaches up to −0.61 during 1979–2018. Associated with the easterly (westerly) phase of the QBO, there is a meridional dipole pattern of zonal wind from the stratosphere to troposphere over the Northwest Pacific in August with the easterly (westerly) anomalies in 25–50°N and westerly (easterly) anomalies in 50–65°N. This meridional zonal‐wind dipole favors the strengthening (weakening) of the tropospheric Japan Sea high in the QBO easterly (westerly) phase, causing an increase (decrease) of the water vapor transportation from the Northwest Pacific to northern China and thus more (less) precipitation in these regions. The finding of this study has import implications for predicting the summer precipitation in northern China in the future.
The Effects of IMF By on the Middle Thermosphere During a Geomagnetically “Quiet” Period at Solar Minimum
Authors: Cai Xuguang , Wang Wenbin , Burns Alan , Qian Liying , Eastes Richard W. 
Published: April 2022

AbstractNumerical simulations using the National Center for Atmospheric Research (NCAR) thermosphere‐ionosphere‐electrodynamics general circulation model (TIE‐GCM) are performed to elucidate the effects of the interplanetary magnetic field (IMF) on the middle thermosphere composition during a “geomagnetically quiet” period from the day of year (DOY) 110–111 in 2019 (when the Auroral electrojet (AE) index never exceeded 300 nT and the Kp never exceeded 2). In particular, this paper aims to examine how the Global‐scale Observations of the Limb and Disk (GOLD) mission observed daytime thermospheric O and N2 column density ratio (∑O/N2) depletion at mid‐latitudes originated under such a “geomagnetically quiet” condition. A comparison of electric potential, Joule heating rate per unit mass, ion velocity, neutral temperature and winds in the middle thermosphere (∼160 km) between real IMF and without the IMF east‐west component (By) indicates that a By dominant condition can enhance their strengths under this “geomagnetically quiet” condition. Consequently, ∑O/N2 depletion with a stronger magnitude (30% compared with ∼8% without By) and larger disturbed area was introduced in the post‐midnight sector at high‐latitudes due to strong and localized upwelling associated with the enhanced Joule heating rate per unit mass. The ∑O/N2 depletion was transported equatorward and corotated from local post‐midnight to early morning, and was observed by GOLD at middle latitudes during daytime.
Wind‐Driven Freshwater Export at Cape Farewell
Authors: Duyck E. , Gelderloos R. , de Jong M. F. 
Published: April 2022

AbstractIncreased freshwater input to the Subpolar North Atlantic from Greenland ice melt and the Arctic could strengthen stratification in deep convection regions and impact the overturning circulation. However, freshwater pathways from the east Greenland shelf to deep convection regions are not fully understood. We investigate the role of strong wind events at Cape Farewell in driving surface freshwaters from the East Greenland Current to the Irminger Sea. Using a high‐resolution model and an atmospheric reanalysis, we identify strong wind events and investigate their impact on freshwater export. Westerly tip jets are associated with the strongest and deepest freshwater export across the shelfbreak, with a mean of 37.5 mSv of freshwater in the first 100 m (with reference salinity 34.9). These wind events tilt isohalines and extend the front offshore, especially over Eirik Ridge. Moderate westerly events are associated with weaker export across the shelfbreak (mean of 15.9 mSv) but overall contribute to more freshwater export throughout the year, including in summer, when the shelf is particularly fresh. Particle tracking shows that half of the surface waters crossing the shelfbreak during tip jet events are exported away from the shelf, either entering the Irminger Gyre, or being driven over Eirik Ridge. During strong westerly wind events, sea ice detaches from the coast and veers toward the Irminger Sea, but the contribution of sea ice to freshwater export at the shelfbreak is minimal compared to liquid freshwater export due to limited sea ice cover at Cape Farewell.
Landslide Processes Involved in Volcano Dismantling From Past to Present: The Remarkable Open‐Air Laboratory of the Cirque de Salazie (Reunion Island)
Authors: Rault C. , Thiery Y. , Chaput M. , Reninger P. A. , Dewez T. J. B. , Michon L. , Samyn K. , Aunay B. 
Published: April 2022

AbstractThe Cirque de Salazie is one of the large erosional depressions of Reunion Island. Composed of a thick accumulation of loose volcaniclastic materials derived from successive volcanic flank collapses and exposed to high precipitation rates, this large depression is particularly prone to landslides. Of the 133 km2 making up this large depression, at least 19% of slopes are affected by various types of landslides. The diversity and high density of landslides is one of the main issues for inhabited areas. We examine the landslides in this area with the goal of providing key elements for better hazard assessment and understanding their role in the landscape's evolution. For over 20 years, we have been acquiring multidisciplinary data on landslides. In this cirque, eight types of landslides are identified and described following an adapted landslide classification. Using a multidisciplinary approach, we characterize and interpret the surface morphology and internal structure of three large inhabited compound landslides with volumes of 0.1 km3 moving up to 1.15 myr−1. These complex landslides provide an opportunity to investigate the influence of past slope movements on current slope movements. Furthermore, using detailed mapping and volume calculation of the landslides triggered by the last major cyclonic rainstorm, we estimate that rainfall‐triggered landslides contribute up to 20% of the long‐term erosion rate. The Cirque de Salazie is a remarkable laboratory that offers new insights and challenges for future research on landslide hazard assessment and the role of landslides in the short‐ and long‐term dismantling of volcanoes.
Ionospheric Phase Scintillation Index Estimation Based on 1 Hz Geodetic GNSS Receiver Measurements by Using Continuous Wavelet Transform
Authors: Zhao Dongsheng , Li Wang , Li Chendong , Tang Xu , Wang Qianxin , Hancock Craig M. , Roberts Gethin Wyn , Zhang Kefei 
Published: April 2022

AbstractThe adverse effect of the ionospheric scintillation on Global Navigation Satellite System (GNSS) requires scintillation monitoring on a global scale. Ionospheric Scintillation Monitoring Receivers (ISMR) are usually adopted to monitor scintillation, while they are not suitable for global monitoring due to the 50 Hz data collecting rate, which restricts the distribution. This paper proposes a new method to extract the phase scintillation index from each GNSS carrier with 1s‐sampling‐interval, mainly based on the cycle slip detection, the geodetic detrending and the wavelet transform, in which the optimal symmetry parameter and the time‐bandwidth product are determined with trial calculation. Taken the index provided by ISMR as the reference, 1‐year observations are utilized to evaluate the scintillation monitoring performance of the extracted index regarding the correlation of the magnitude in each observation arc, the detected daily scintillation occurrence rate, the diurnal variation pattern of the ionospheric scintillation, the correlation between the scintillation occurrence rate and the space weather parameter, and the complementary cumulative distribution of the magnitudes. Compared to the performance of Rate of Total electron content Index, a higher consistency can be achieved between the extracted index and the index, indicating the rationality of applying the proposed method in monitoring scintillations. The extracted scintillation index can be expected to introduce geodetic receivers operating at 1s‐sampling‐interval into the field of ionospheric scintillation monitoring on a global scale.
Physics‐Informed Machine Learning Method for Large‐Scale Data Assimilation Problems
Authors: Yeung Yu‐Hong , Barajas‐Solano David A. , Tartakovsky Alexandre M. 
Published: April 2022

AbstractWe develop a physics‐informed machine learning approach for large‐scale data assimilation and parameter estimation and apply it for estimating transmissivity and hydraulic head in the two‐dimensional steady‐state subsurface flow model of the Hanford Site given synthetic measurements of said variables. In our approach, we extend the physics‐informed conditional Karhunen‐Loéve expansion (PICKLE) method to modeling subsurface flow with unknown flux (Neumann) and varying head (time‐dependent Dirichlet) boundary conditions. We demonstrate that the PICKLE method is comparable in accuracy with the standard maximum a posteriori (MAP) method, but is significantly faster than MAP for large‐scale problems. Both methods use a mesh to discretize the computational domain. In MAP, the parameters and states are discretized on the mesh; therefore, the size of the MAP parameter estimation problem directly depends on the mesh size. In PICKLE, the mesh is used to evaluate the residuals of the governing equation, while the parameters and states are approximated by the truncated conditional Karhunen‐Loéve expansions with the number of parameters controlled by the smoothness of the parameter and state fields, and not by the mesh size. For a considered example, we demonstrate that the computational cost of PICKLE increases near linearly (as N1.15) with the number of grid nodes N, while that of MAP increases much faster (as N3.28). We also show that once trained for one set of Dirichlet boundary conditions (i.e., one river stage), the PICKLE method provides accurate estimates of the hydraulic head for any value of the Dirichlet boundary conditions (i.e., for any river stage).
Solar Flux Influence on the In‐Situ Plasma Density at Topside Ionosphere Measured by Swarm Satellites
Authors: Xiong Chao , Jiang Haicheng , Yan Rui , Lühr Hermann , Stolle Claudia , Yin Fan , Smirnov Artem , Piersanti Mirko , Liu Yiwen , Wan Xin , Diego Piero , Zhima Zeren , Shen Xuhui , Förster Matthias , Buchert Stephan , Bilitza Dieter 
Published: April 2022

AbstractIn this study, we perform the first comprehensive comparison of ion density (Ni) in the topside ionosphere measured by the Langmuir probe (LP) and faceplate (FP) of the thermal ion imager on board Swarm satellites. Our results show a systematic difference between the LP and FP derived Ni values, and the systematic difference shows prominent dependences on solar flux, local time, and season. Although both Ni datasets show generally good linear regression with electron density (Ne) measurements from the incoherent scatter radar (ISR) located at Jicamarca, the Ni derived from LP shows an additional dependence on the solar flux, while such a dependence cannot be seen in the FP‐derived Ni. We suggest that the solar flux dependence of LP‐derived Ni is related to the ion compositions change at Swarm altitude, which has not been properly accounted for in the LP processing algorithm. More light ions (e.g., H+), diffusing down from the plasmasphere to the Swarm altitude, seem to cause the overestimation of Ni from LP during low solar activity. A linear relation between the Swarm LP‐derived Ni and ISR Ne is derived, and such a function is recommended to be implemented into further updates of the Swarm LP plasma density data.
Integrated clinical and genomic evaluation of guadecitabine (SGI-110) in peripheral T-cell lymphoma
Authors: Wong Jonathan , Gruber Emily , Maher Belinda , Waltham Mark , Sabouri-Thompson Zahra , Jong Ian , Luong Quinton , Levy Sidney , Kumar Beena , Brasacchio Daniella , Jia Wendy , So Joan , Skinner Hugh , Lewis Alexander , Hogg Simon J. , Vervoort Stephin , DiCorleto Carmen , Uhe Micheleine , Gamgee Jeanette , Opat Stephen , Gregory Gareth P. , Polekhina Galina , Reynolds John , Hawkes Eliza A. , Kailainathan Gajan , Gasiorowski Robin , Kats Lev M. , Shortt Jake 
Published: April 2022

AbstractPeripheral T-cell lymphoma (PTCL) is a rare, heterogenous malignancy with dismal outcomes at relapse. Hypomethylating agents (HMA) have an emerging role in PTCL, supported by shared mutations with myelodysplasia (MDS). Response rates to azacitidine in PTCL of follicular helper cell origin are promising. Guadecitabine is a decitabine analogue with efficacy in MDS. In this phase II, single-arm trial, PTCL patients received guadecitabine on days 1–5 of 28-day cycles. Primary end points were overall response rate (ORR) and safety. Translational sub-studies included cell free plasma DNA sequencing and functional genomic screening using an epigenetically-targeted CRISPR/Cas9 library to identify response predictors. Among 20 predominantly relapsed/refractory patients, the ORR was 40% (10% complete responses). Most frequent grade 3-4 adverse events were neutropenia and thrombocytopenia. At 10 months median follow-up, median progression free survival (PFS) and overall survival (OS) were 2.9 and 10.4 months respectively. RHOAG17V mutations associated with improved PFS (median 5.47 vs. 1.35 months; Wilcoxon p = 0.02, Log-Rank p = 0.06). 4/7 patients with TP53 variants responded. Deletion of the histone methyltransferase SETD2 sensitised to HMA but TET2 deletion did not. Guadecitabine conveyed an acceptable ORR and toxicity profile; decitabine analogues may provide a backbone for future combinatorial regimens co-targeting histone methyltransferases.
TCRP1 activated by mutant p53 promotes NSCLC proliferation via inhibiting FOXO3a
Authors: Liu Hao , Jia Xiaoting , Luo Kai , Chen Xiangzhou , Zhang Zhijie , Chen Danyang , Gu Yixue , He Zhimin , Zheng Guopei 
Published: April 2022

AbstractPreviously, our lab explored that tongue cancer resistance-associated protein (TCRP1) plays a central role in cancer chemo-resistance and progression. Absolutely, TCRP1 was significantly increased in lung cancer. But the mechanism is far from elucidated. Here, we found that TCRP1 was increased in p53-mutant non-small-cell lung cancer (NSCLC), comparing to that in NSCLC with wild type p53. Further study showed that mutant p53 couldn’t bind to the promoter of TCRP1 to inhibit its expression. While the wild type p53 did so. Next, loss-and gain-of-function assays demonstrated that TCRP1 promoted cell proliferation and tumor growth in NSCLC. Regarding the mechanism, TCRP1 encouraged AKT phosphorylation and blocked FOXO3a nuclear localization through favoring FOXO3a ubiquitination in cytoplasm, thus, promoted cell cycle progression. Conclusionly, TCRP1 was upregulated in NSCLC cells with mutant p53. TCRP1 promoted NSCLC progression via regulating cell cycle.
Fusion protein-driven IGF-IR/PI3K/AKT signals deregulate Hippo pathway promoting oncogenic cooperation of YAP1 and FUS-DDIT3 in myxoid liposarcoma
Authors: Berthold Ruth , Isfort Ilka , Erkut Cihan , Heinst Lorena , Grünewald Inga , Wardelmann Eva , Kindler Thomas , Åman Pierre , Grünewald Thomas G. P. , Cidre-Aranaz Florencia , Trautmann Marcel , Fröhling Stefan , Scholl Claudia , Hartmann Wolfgang 
Published: April 2022

AbstractMyxoid liposarcoma (MLS) represents a common subtype of liposarcoma molecularly characterized by a recurrent chromosomal translocation that generates a chimeric FUS-DDIT3 fusion gene. The FUS-DDIT3 oncoprotein has been shown to be crucial in MLS pathogenesis. Acting as a transcriptional dysregulator, FUS-DDIT3 stimulates proliferation and interferes with adipogenic differentiation. As the fusion protein represents a therapeutically challenging target, a profound understanding of MLS biology is elementary to uncover FUS-DDIT3-dependent molecular vulnerabilities. Recently, a specific reliance on the Hippo pathway effector and transcriptional co-regulator YAP1 was detected in MLS; however, details on the molecular mechanism of FUS-DDIT3-dependent YAP1 activation, and YAP1´s precise mode of action remain unclear. In elaborate in vitro studies, employing RNA interference-based approaches, small-molecule inhibitors, and stimulation experiments with IGF-II, we show that FUS-DDIT3-driven IGF-IR/PI3K/AKT signaling promotes stability and nuclear accumulation of YAP1 via deregulation of the Hippo pathway. Co-immunoprecipitation and proximity ligation assays revealed nuclear co-localization of FUS-DDIT3 and YAP1/TEAD in FUS-DDIT3-expressing mesenchymal stem cells and MLS cell lines. Transcriptome sequencing of MLS cells demonstrated that FUS-DDIT3 and YAP1 co-regulate oncogenic gene signatures related to proliferation, cell cycle progression, apoptosis, and adipogenesis. In adipogenic differentiation assays, we show that YAP1 critically contributes to FUS-DDIT3-mediated adipogenic differentiation arrest. Taken together, our study provides mechanistic insights into a complex FUS-DDIT3-driven network involving IGF-IR/PI3K/AKT signals acting on Hippo/YAP1, and uncovers substantial cooperative effects of YAP1 and FUS-DDIT3 in the pathogenesis of MLS.
AAV-ie-K558R mediated cochlear gene therapy and hair cell regeneration
Authors: Tao Yong , Liu Xiaoyi , Yang Liu , Chu Cenfeng , Tan Fangzhi , Yu Zehua , Ke Junzi , Li Xiang , Zheng Xiaofei , Zhao Xingle , Qi Jieyu , Lin Chao-Po , Chai Renjie , Zhong Guisheng , Wu Hao 
Published: April 2022

AbstractThe cochlea consists of multiple types of cells, including hair cells, supporting cells and spiral ganglion neurons, and is responsible for converting mechanical forces into electric signals that enable hearing. Genetic and environmental factors can result in dysfunctions of cochlear and auditory systems. In recent years, gene therapy has emerged as a promising treatment in animal deafness models. One major challenge of the gene therapy for deafness is to effectively deliver genes to specific cells of cochleae. Here, we screened and identified an AAV-ie mutant, AAV-ie-K558R, that transduces hair cells and supporting cells in the cochleae of neonatal mice with high efficiency. AAV-ie-K558R is a safe vector with no obvious deficits in the hearing system. We found that AAV-ie-K558R can partially restore the hearing loss in Prestin KO mice and, importantly, deliver Atoh1 into cochlear supporting cells to generate hair cell-like cells. Our results demonstrate the clinical potential of AAV-ie-K558R for treating the hearing loss caused by hair cell death.