bluuebunny/crossref_metadata_2025_split huggingface dataset:
Afterslip Moment Scaling and Variability From a Global Compilation of Estimates
Authors: Churchill R. M. , Werner M. J. , Biggs J. , Fagereng Å. 
Published: April 2022

AbstractAseismic afterslip is postseismic fault sliding that may significantly redistribute crustal stresses and drive aftershock sequences. Afterslip is typically modeled through geodetic observations of surface deformation on a case‐by‐case basis, thus questions of how and why the afterslip moment varies between earthquakes remain largely unaddressed. We compile 148 afterslip studies following 53Mw6.0–9.1 earthquakes, and formally analyze a subset of 88 well‐constrained kinematic models. Afterslip and coseismic moments scale near‐linearly, with a median Spearman's rank correlation coefficient (CC) of 0.91 after bootstrapping (95% range: 0.89–0.93). We infer that afterslip area and average slip scale with coseismic moment asand, respectively. The ratio of afterslip to coseismic moment (Mrel) varies from <1% to >300% (interquartile range: 9%–32%).Mrelweakly correlates withMo(CC: −0.21, attributed to a publication bias), rupture aspect ratio (CC: −0.31), and fault slip rate (CC: 0.26, treated as a proxy for fault maturity), indicating that these factors affect afterslip.Mreldoes not correlate with mainshock dip, rake, or depth. Given the power‐law decay of afterslip, we expected studies that started earlier and spanned longer timescales to capture more afterslip, butMreldoes not correlate with observation start time or duration. BecauseMrelestimates for a single earthquake can vary by an order of magnitude, we propose that modeling uncertainty currently presents a challenge for systematic afterslip analysis. Standardizing modeling practices may improve model comparability, and eventually allow for predictive afterslip models that account for mainshock and fault zone factors to be incorporated into aftershock hazard models.
Climate Change Impacts to the Arctic Ocean Revealed From High Resolution GEOTRACES 210Po‐210Pb‐226Ra Disequilibria Studies
Authors: Baskaran M. , Krupp K. , Bam W. , Maiti K. 
Published: April 2022

AbstractClimate change is transforming the Arctic Ocean in unprecedented ways which can be most directly observed in the systematic decline in seasonal ice coverage. From the collection and analysis of particulate and dissolved activities of 210Po and 210Pb from four deepwater superstations, as a part of the US Arctic GEOTRACES cruise during 2015, and in conjunction with previously published data, the temporal and spatial variations in their activities, inventories and residence times are evaluated. The results show that the partitioning of particulate and dissolved phases has changed significantly in the 8 years between 2007 and 2015, while the total 210Po and 210Pb activities have remained relatively unchanged. Observed total 210Po/210Pb activity ratio was less than unity in all deepwater stations, implying disequilibria in the entire water column. From the distribution of total 210Po and 210Pb in the upper 500 m of all major Arctic Basins, the derived scavenging efficiencies decrease as per the following sequence: Makarov Basin > Gakkel Bridge > Canada Basin Nansen Basin ∼ Amundsen Basin > Alpha Ridge, which is the reverse order of the calculated residence times of 210PoT. The scavenging intensities differ between the fully ice‐covered, partially ice‐covered, and no ice‐covered stations, as observed from the differences in the average activities of 210Po and 210Pb. The average settling velocity of particulate matter based on the 210Pb activity is similar to the published values based on 230Th, indicating removal mechanism(s) of Th and Pb is (are) similar.
Architecture of the human NALCN channelosome
Authors: Zhou Lunni , Liu Haobin , Zhao Qingqing , Wu Jianping , Yan Zhen 
Published: April 2022

AbstractNALCN regulates the resting membrane potential by mediating the Na+ leak current in neurons, and it functions as a channelosome in complex with FAM155A, UNC79, and UNC80. Dysfunction of the NALCN channelosome causes a broad range of neurological and developmental diseases called NALCN channelopathies in humans. How the auxiliary subunits, especially the two large components UNC79 and UNC80, assemble with NALCN and regulate its function remains unclear. Here we report an overall architecture of the human NALCN channelosome. UNC79 and UNC80 each adopt an S-shape super-helical structure consisting of HEAT and armadillo repeats, forming a super-coiled heterodimeric assembly in the cytoplasmic side, which may provide a scaffold for the binding of other potential modulators of the channelosome. The UNC79–UNC80 assembly specifically associates with the NALCN–FAM155A subcomplex through the intracellular II–III linker of NALCN. Disruptions of the interaction interfaces between UNC79 and UNC80, and between the II–III linker of NALCN and the UNC79–UNC80 assembly, significantly reduce the NALCN-mediated currents in HEK293T system, suggesting the importance of the UNC79–UNC80 assembly in regulating channelosome function. Cross-linking mass spectrometry analysis identified an additional calmodulin (CaM) bound in the carboxyl-terminal domain of NALCN. Our study thus provides a structural basis for understanding the unique assembly mechanism and functional regulation of the NALCN channelosome, and also provides an opportunity for the interpretation of many disease-related mutations in UNC80.
Metal-responsive regulation of enzyme catalysis using genetically encoded chemical switches
Authors: Zubi Yasmine S. , Seki Kosuke , Li Ying , Hunt Andrew C. , Liu Bingqing , Roux Benoît , Jewett Michael C. , Lewis Jared C. 
Published: April 2022

AbstractDynamic control over protein function is a central challenge in synthetic biology. To address this challenge, we describe the development of an integrated computational and experimental workflow to incorporate a metal-responsive chemical switch into proteins. Pairs of bipyridinylalanine (BpyAla) residues are genetically encoded into two structurally distinct enzymes, a serine protease and firefly luciferase, so that metal coordination biases the conformations of these enzymes, leading to reversible control of activity. Computational analysis and molecular dynamics simulations are used to rationally guide BpyAla placement, significantly reducing experimental workload, and cell-free protein synthesis coupled with high-throughput experimentation enable rapid prototyping of variants. Ultimately, this strategy yields enzymes with a robust 20-fold dynamic range in response to divalent metal salts over 24 on/off switches, demonstrating the potential of this approach. We envision that this strategy of genetically encoding chemical switches into enzymes will complement other protein engineering and synthetic biology efforts, enabling new opportunities for applications where precise regulation of protein function is critical.
Activation of the essential kinase PDK1 by phosphoinositide-driven trans-autophosphorylation
Authors: Levina Aleksandra , Fleming Kaelin D. , Burke John E. , Leonard Thomas A. 
Published: April 2022

Abstract3-phosphoinositide-dependent kinase 1 (PDK1) is an essential serine/threonine protein kinase, which plays a crucial role in cell growth and proliferation. It is often referred to as a ‘master’ kinase due to its ability to activate at least 23 downstream protein kinases implicated in various signaling pathways. In this study, we have elucidated the mechanism of phosphoinositide-driven PDK1 auto-activation. We show that PDK1 trans-autophosphorylation is mediated by a PIP3-mediated face-to-face dimer. We report regulatory motifs in the kinase-PH interdomain linker that allosterically activate PDK1 autophosphorylation via a linker-swapped dimer mechanism. Finally, we show that PDK1 is autoinhibited by its PH domain and that positive cooperativity of PIP3 binding drives switch-like activation of PDK1. These results imply that the PDK1-mediated activation of effector kinases, including Akt, PKC, Sgk, S6K and RSK, many of whom are not directly regulated by phosphoinositides, is also likely to be dependent on PIP3 or PI(3,4)P2.
Depletion of tumor associated macrophages enhances local and systemic platelet-mediated anti-PD-1 delivery for post-surgery tumor recurrence treatment
Authors: Li Zhaoting , Ding Yingyue , Liu Jun , Wang Jianxin , Mo Fanyi , Wang Yixin , Chen-Mayfield Ting-Jing , Sondel Paul M. , Hong Seungpyo , Hu Quanyin 
Published: April 2022

AbstractImmunosuppressive cells residing in the tumor microenvironment, especially tumor associated macrophages (TAMs), hinder the infiltration and activation of T cells, limiting the anti-cancer outcomes of immune checkpoint blockade. Here, we report a biocompatible alginate-based hydrogel loaded with Pexidartinib (PLX)-encapsulated nanoparticles that gradually release PLX at the tumor site to block colony-stimulating factor 1 receptors (CSF1R) for depleting TAMs. The controlled TAM depletion creates a favorable milieu for facilitating local and systemic delivery of anti-programmed cell death protein 1 (aPD-1) antibody-conjugated platelets to inhibit post-surgery tumor recurrence. The tumor immunosuppressive microenvironment is also reprogrammed by TAM elimination, further promoting the infiltration of T cells into tumor tissues. Moreover, the inflammatory environment after surgery could trigger the activation of platelets to facilitate the release of aPD-1 accompanied with platelet-derived microparticles binding to PD-1 receptors for re-activating T cells. All these results collectively indicate that the immunotherapeutic efficacy against tumor recurrence of both local and systemic administration of aPD-1 antibody-conjugated platelets could be strengthened by local depletion of TAMs through the hydrogel reservoir.
Direct sound printing
Authors: Habibi Mohsen , Foroughi Shervin , Karamzadeh Vahid , Packirisamy Muthukumaran 
Published: April 2022

AbstractPhoto- and thermo-activated reactions are dominant in Additive Manufacturing (AM) processes for polymerization or melting/deposition of polymers. However, ultrasound activated sonochemical reactions present a unique way to generate hotspots in cavitation bubbles with extraordinary high temperature and pressure along with high heating and cooling rates which are out of reach for the current AM technologies. Here, we demonstrate 3D printing of structures using acoustic cavitation produced directly by focused ultrasound which creates sonochemical reactions in highly localized cavitation regions. Complex geometries with zero to varying porosities and 280 μm feature size are printed by our method, Direct Sound Printing (DSP), in a heat curing thermoset, Poly(dimethylsiloxane) that cannot be printed directly so far by any method. Sonochemiluminescnce, high speed imaging and process characterization experiments of DSP and potential applications such as remote distance printing are presented. Our method establishes an alternative route in AM using ultrasound as the energy source.
Elastic dosage compensation by X-chromosome upregulation
Authors: Lentini Antonio , Cheng Huaitao , Noble J. C. , Papanicolaou Natali , Coucoravas Christos , Andrews Nathanael , Deng Qiaolin , Enge Martin , Reinius Björn 
Published: April 2022

AbstractX-chromosome inactivation and X-upregulation are the fundamental modes of chromosome-wide gene regulation that collectively achieve dosage compensation in mammals, but the regulatory link between the two remains elusive and the X-upregulation dynamics are unknown. Here, we use allele-resolved single-cell RNA-seq combined with chromatin accessibility profiling and finely dissect their separate effects on RNA levels during mouse development. Surprisingly, we uncover that X-upregulation elastically tunes expression dosage in a sex- and lineage-specific manner, and moreover along varying degrees of X-inactivation progression. Male blastomeres achieve X-upregulation upon zygotic genome activation while females experience two distinct waves of upregulation, upon imprinted and random X-inactivation; and ablation of Xist impedes female X-upregulation. Female cells carrying two active X chromosomes lack upregulation, yet their collective RNA output exceeds that of a single hyperactive allele. Importantly, this conflicts the conventional dosage compensation model in which naïve female cells are initially subject to biallelic X-upregulation followed by X-inactivation of one allele to correct the X dosage. Together, our study provides key insights to the chain of events of dosage compensation, explaining how transcript copy numbers can remain remarkably stable across developmental windows wherein severe dose imbalance would otherwise be experienced by the cell.
Accurate auto-labeling of chest X-ray images based on quantitative similarity to an explainable AI model
Authors: Kim Doyun , Chung Joowon , Choi Jongmun , Succi Marc D. , Conklin John , Longo Maria Gabriela Figueiro , Ackman Jeanne B. , Little Brent P. , Petranovic Milena , Kalra Mannudeep K. , Lev Michael H. , Do Synho 
Published: April 2022

AbstractThe inability to accurately, efficiently label large, open-access medical imaging datasets limits the widespread implementation of artificial intelligence models in healthcare. There have been few attempts, however, to automate the annotation of such public databases; one approach, for example, focused on labor-intensive, manual labeling of subsets of these datasets to be used to train new models. In this study, we describe a method for standardized, automated labeling based on similarity to a previously validated, explainable AI (xAI) model-derived-atlas, for which the user can specify a quantitative threshold for a desired level of accuracy (the probability-of-similarity, pSim metric). We show that our xAI model, by calculating the pSim values for each clinical output label based on comparison to its training-set derived reference atlas, can automatically label the external datasets to a user-selected, high level of accuracy, equaling or exceeding that of human experts. We additionally show that, by fine-tuning the original model using the automatically labelled exams for retraining, performance can be preserved or improved, resulting in a highly accurate, more generalized model.
Quantum dot-integrated GaN light-emitting diodes with resolution beyond the retinal limit
Authors: Bae Junho , Shin Yuseop , Yoo Hyungyu , Choi Yongsu , Lim Jinho , Jeon Dasom , Kim Ilsoo , Han Myungsoo , Lee Seunghyun 
Published: April 2022

AbstractNear-eye display technology is a rapidly growing field owing to the recent emergence of augmented and mixed reality. Ultrafast response time, high resolution, high luminance, and a dynamic range for outdoor use are all important for non-pixelated, pupil-forming optics. The current mainstream technologies using liquid crystals and organic materials cannot satisfy all these conditions. Thus, finely patterned light-emissive solid-state devices with integrated circuits are often proposed to meet these requirements. In this study, we integrated several advanced technologies to design a prototype microscale light-emitting diode (LED) arrays using quantum dot (QD)-based color conversion. Wafer-scale epilayer transfer and the bond-before-pattern technique were used to directly integrate 5-µm-scale GaN LED arrays on a foreign silicon substrate. Notably, the lithography-level alignment with the bottom wafer opens up the possibility for ultrafast operation with circuit integration. Spectrally pure color conversion and solvent-free QD patterning were also achieved using an elastomeric topographical mask. Self-assembled monolayers were applied to selectively alter the surface wettability for a completely dry process. The final emissive-type LED array integrating QD, GaN, and silicon technology resulted in a 1270 PPI resolution that is far beyond the retinal limit.
STAG2 regulates interferon signaling in melanoma via enhancer loop reprogramming
Authors: Chu Zhaowei , Gu Lei , Hu Yeguang , Zhang Xiaoyang , Li Man , Chen Jiajia , Teng Da , Huang Man , Shen Che-Hung , Cai Li , Yoshida Toshimi , Qi Yifeng , Niu Zhixin , Feng Austin , Geng Songmei , Frederick Dennie T. , Specht Emma , Piris Adriano , Sullivan Ryan J. , Flaherty Keith T. , Boland Genevieve M. , Georgopoulos Katia , Liu David , Shi Yang , Zheng Bin 
Published: April 2022

AbstractThe cohesin complex participates in the organization of 3D genome through generating and maintaining DNA loops. Stromal antigen 2 (STAG2), a core subunit of the cohesin complex, is frequently mutated in various cancers. However, the impact of STAG2 inactivation on 3D genome organization, especially the long-range enhancer-promoter contacts and subsequent gene expression control in cancer, remains poorly understood. Here we show that depletion of STAG2 in melanoma cells leads to expansion of topologically associating domains (TADs) and enhances the formation of acetylated histone H3 lysine 27 (H3K27ac)-associated DNA loops at sites where binding of STAG2 is switched to its paralog STAG1. We further identify Interferon Regulatory Factor 9 (IRF9) as a major direct target of STAG2 in melanoma cells via integrated RNA-seq, STAG2 ChIP-seq and H3K27ac HiChIP analyses. We demonstrate that loss of STAG2 activates IRF9 through modulating the 3D genome organization, which in turn enhances type I interferon signaling and increases the expression of PD-L1. Our findings not only establish a previously unknown role of the STAG2 to STAG1 switch in 3D genome organization, but also reveal a functional link between STAG2 and interferon signaling in cancer cells, which may enhance the immune evasion potential in STAG2-mutant cancer.
Geostatistical spatial projection of geophysical parameters for practical aquifer mapping
Authors: Dabas Jagriti , Sarah Sarah , Mondal N. C. , Ahmed Shakeel 
Published: April 2022

AbstractDense data acquisition for 3-D high-resolution aquifer mapping through heliborne transient electromagnetic (HTEM) survey is continually not possible due to various technical and administrative constraints. Consequently, we apply ground geophysical surveys at possibly closer spacing to collect the sub-surface information in the no-fly area, which provides only a regional aquifer picture. In the area near Patna of Northern India, an extent of 18% was covered under the HTEM survey, and the rest was surveyed by ground geophysical methods. Both data are integrated using the theory of regionalized variables. The parameters of multi-aquifers i.e., top of the first aquifer, top of the separating clay layer, top and the bottom of second aquifer, are estimated together with their respective resistivities. The estimations are made at an interval of 250 m, practically an appropriate distance at which dense data generation was carried out using the HTEM survey. The integrated approach generates the data in the no-fly area with the same spatial density as the flown area. With this, we achieved the goal of completing the 3-D aquifer mapping of the entire area with dense data at high spatial resolution. This is a unique finding to manage the handicapped situation in this HTEM surveys, and an aide to overcome such constraints with cost-effectiveness.
Mechanical and microstructural performance of concrete containing high-volume of bagasse ash and silica fume
Authors: Amin Muhammad Nasir , Ahmad Afaq , Shahzada Khan , Khan Kaffayatullah , Jalal Fazal E. , Qadir Muhammad Ghulam 
Published: April 2022

AbstractIn this study, researchers examined the effect of replacing a high-volume of cement with sugarcane bagasse ash (BA) and silica fume (SF). In addition to the control, three binary and three ternary blends of concrete containing different percentages of cement/BA and cement/BA/SF were tested to determine the various mechanical and microstructural properties of concrete. For each mix, eighteen cylindrical concrete specimens were cast followed by standard curing (moist at 20 °C) to test the compressive and tensile strengths of three identical specimens at 7, 28, and 91 days. The test results indicated that the binary mix with 20% BA and ternary mix with 33% BA and 7% SF exhibited higher strengths than all the other mixes, including the control. The higher strengths of these mixes are also validated by their lower water absorption and apparent porosity than the other mixes. Following mechanical testing, the micro and pore structures of all mixes were investigated by performing scanning electron microscopy/energy-dispersive X-ray spectroscopy (SEM–EDS), Fourier transform infrared (FTIR) spectroscopy, thermogravimetric analysis (TGA), and nitrogen (N2) adsorption isotherm analysis. In SEM–EDS analysis, a dense and compact microstructure was observed for the BA20 and BA33SF7 mixtures due to the formation of high-density C–S–H and C–H phases. The formation of a large amount of C–S–H phases was observed through FTIR, where a prominent shift in peaks from 955 to 970 cm−1 was observed in the spectra of these mixes. Moreover, in N2 adsorption isotherm analysis, a decrease in the intruded pore volume and an increase in the BET surface area of the paste matrix indicate the densification of the pore structure of these mixes. As observed through TGA, a reduction in the amount of the portlandite phase in these mixes leads to the formation of their more densified micro and pore structures. The current findings indicate that BA (20%) and its blend with SF (40%) represents a potential revenue stream for the development of sustainable and high-performance concretes in the future.
Global analysis of a time fractional order spatio-temporal SIR model
Authors: Sidi Ammi Moulay Rchid , Tahiri Mostafa , Tilioua Mouhcine , Zeb Anwar , Khan Ilyas , Andualem Mulugeta 
Published: April 2022

AbstractWe deal in this paper with a diffusive SIR epidemic model described by reaction–diffusion equations involving a fractional derivative. The existence and uniqueness of the solution are shown, next to the boundedness of the solution. Further, it has been shown that the global behavior of the solution is governed by the value of $$R_0$$

R
0

, which is known in epidemiology by the basic reproduction number. Indeed, using the Lyapunov direct method it has been proved that the disease will extinct for $$ R_0 <1 $$

R
0

<
1

for any value of the diffusion constants. For $$R_0>1$$

R
0

>
1

, the disease will persist and the unique positive equilibrium is globally stable. Some numerical illustrations have been used to confirm our theoretical results.