bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characteristics of Slow Slip Events Explained by Rate‐Strengthening Faults Subject to Periodic Pore Fluid Pressure Changes
Authors: Perez‐Silva Andrea , Kaneko Yoshihiro , Savage Martha , Wallace Laura , Warren‐Smith Emily 
Published: June 2023

AbstractGeophysical observations suggest that temporal changes in pore fluid pressure correlate with slow slip events (SSEs) at some subduction zones, including the Hikurangi and Cascadia subduction zones. These fluctuations in pore fluid pressure are attributed to fluid migration before and during SSEs, which may modulate SSE occurrence. To examine the effect of pore fluid pressure changes on SSE generation, we develop numerical models in which periodic pore‐pressure perturbations are applied to a stably sliding, rate‐strengthening fault. By varying the physical characteristics of the pore‐pressure perturbations (amplitude, characteristic length and period), we find models that reproduce shallow Hikurangi SSE properties (duration, magnitude, slip, recurrence) and SSE moments and durations from different subduction zones. The stress drops of modeled SSEs range from ∼20–120 kPa while the amplitudes of pore‐pressure perturbations are several MPa, broadly consistent with those inferred from observations. Our results indicate that large permeability values of ∼10−14 to 10−10 m2 are needed to reproduce the observed SSE properties. Such high values could be due to transient and localized increases in fault zone permeability in the shear zone where SSEs occur. Our results suggest that SSEs may arise on faults in rate‐strengthening frictional conditions subject to pore‐pressure perturbations.
Do State‐Of‐The‐Art Atmospheric CO2 Inverse Models Capture Drought Impacts on the European Land Carbon Uptake?
Authors: He Wei , Jiang Fei , Ju Weimin , Byrne Brendan , Xiao Jingfeng , Nguyen Ngoc Tu , Wu Mousong , Wang Songhan , Wang Jun , Rödenbeck Christian , Li Xing , Scholze Marko , Monteil Guillaume , Wang Hengmao , Zhou Yanlian , He Qiaoning , Chen Jing M. 
Published: June 2023

AbstractThe European land carbon uptake has been heavily impacted by several recent severe droughts, yet quantitative estimates of carbon uptake anomalies are uncertain. Atmospheric CO2 inverse models (AIMs) provide observation‐based estimates of the large‐scale carbon flux dynamics, but how well they capture drought impacts on the terrestrial carbon uptake is poorly known. Here we assessed the capacity of state‐of‐the‐art AIMs in monitoring drought impacts on the European carbon uptake over 2001–2015 using observations of environmental variability and vegetation function and made comparisons with bottom‐up estimates of carbon uptake anomalies. We found that global inversions with only limited surface CO2 observations give divergent estimates of drought impacts. Regional inversions assimilating denser CO2 observations over Europe demonstrated some improved consistency, with all inversions capturing a reduction in carbon uptake during the 2012 drought. However, they failed to capture the reduction caused by the 2015 drought. Finally, we found that a set of inversions that assimilated satellite XCO2 or assimilated environmental variables plus surface CO2 observations better captured carbon uptake anomalies induced by both the 2012 and 2015 droughts. In addition, the recent Orbiting Carbon Observatory—2 XCO2 inversions showed good potential in capturing drought impacts, with better performances for larger‐scale droughts like the 2018 drought. These results suggest that surface CO2 observations may still be too sparse to fully capture the impact of drought on the carbon cycle at subcontinental scales over Europe, and satellite XCO2 and ancillary environmental data can be used to improve observational constraints in atmospheric inversion systems.
Predicting Marine In Situ Heat Flow Using a Geospatial Machine Learning Conformal Prediction
Authors: Graw J. H. , Wood W. T. , Phrampus B. J. 
Published: June 2023

AbstractHeat flow measurements over the past decades have drastically increased in number. However, even with vast increases in measurements, large geospatial gaps exist, most notably across Earth's oceans. As marine heat flow data acquisition can be tedious, time consuming, and ultimately expensive, new methods have arisen in an attempt to quantify heat flow across the seafloor using empirical proxies. The goal herein is to obtain a high quality, fully data‐driven, global estimate of marine in situ heat flow with calculated uncertainty. We present a heat flow analysis for Earth's marine environment using a geospatial machine learning algorithm (MLA) utilizing 33,746 heat flow measurements from the International Heat Flow Commission's most recent Global Heat Flow Database. The mean heat flow for the observational data set is 95.83 mWm−2 with a spatially averaged heat loss of 40.7 TW. We use a random forest regression MLA combined with a conformal prediction to predict in situ heat flow and its associated uncertainty for marine environments at a 100 km2 global resolution. Ten‐fold cross‐validation yields an R2 value of 0.4, indicating predictive skill. Geospatial prediction results in a global marine surface weighted in situ heat flow average of 69.67 ± 20.01 mWm−2 with a corresponding heat loss of 29.59 ± 5.78 TW. Additionally, parametric isolation is calculated to highlight areas where additional heat flow measurements would be beneficial to directly improve the overall prediction. The resultant in situ heat flow and parametric isolation maps serve as a tool to further heat flow studies within the community.
Symmetry in Hillslope Steepness and Saprolite Thickness Between Hillslopes With Opposing Aspects
Authors: Donaldson A. M. , Zimmer M. , Huang M.‐H. , Johnson K. N. , Hudson‐Rasmussen B. , Finnegan N. , Barling N. , Callahan R. P. 
Published: June 2023

AbstractThe structure of the critical zone (CZ) is a product of feedbacks among hydrologic, climatic, biotic, and chemical processes. Past research within snow‐dominated systems has shown that aspect‐dependent solar radiation inputs can produce striking differences in vegetation composition, topography, and soil depth between opposing hillslopes. However, far fewer studies have evaluated the role of microclimates on CZ development within rain‐dominated systems, especially below the soil and into weathered bedrock. To address this need, we characterized the CZ of a north‐facing and south‐facing slope within a first‐order headwater catchment located in central coast California. We combined terrain analysis of vegetation distribution and topography with soil pit characterization, geophysical surveys and hydrologic measurements between slope‐aspects. We documented denser vegetation and higher shallow soil moisture on north facing slopes, which matched previously documented observations in snow‐dominated sites. However, average topographic gradients were 24° and saprolite thickness was approximately 6 m across both hillslopes, which did not match common observations from the literature that showed widespread asymmetry in snow‐dominated systems. These results suggest that dominant processes for CZ evolution are not necessarily transferable across regions. Thus, there is a continued need to expand CZ research, especially in rain‐dominated and water‐limited systems. Here, we present two non‐exclusive mechanistic hypotheses that may explain these unexpected similarities in slope and saprolite thickness between hillslopes with opposing aspects.
CUL4B orchestrates mesenchymal stem cell commitment by epigenetically repressing KLF4 and C/EBPδ
Authors: Yu Ruiqi , Han Hong , Chu Shuxian , Ding Yijun , Jin Shiqi , Wang Yufeng , Jiang Wei , Liu Yuting , Zou Yongxin , Wang Molin , Liu Qiao , Sun Gongping , Jiang Baichun , Gong Yaoqin 
Published: June 2023

AbstractDysregulated lineage commitment of mesenchymal stem cells (MSCs) contributes to impaired bone formation and an imbalance between adipogenesis and osteogenesis during skeletal aging and osteoporosis. The intrinsic cellular mechanism that regulates MSC commitment remains unclear. Here, we identified Cullin 4B (CUL4B) as a critical regulator of MSC commitment. CUL4B is expressed in bone marrow MSCs (BMSCs) and downregulated with aging in mice and humans. Conditional knockout of Cul4b in MSCs resulted in impaired postnatal skeletal development with low bone mass and reduced bone formation. Moreover, depletion of CUL4B in MSCs aggravated bone loss and marrow adipose accumulation during natural aging or after ovariectomy. In addition, CUL4B deficiency in MSCs reduced bone strength. Mechanistically, CUL4B promoted osteogenesis and inhibited adipogenesis of MSCs by repressing KLF4 and C/EBPδ expression, respectively. The CUL4B complex directly bound to Klf4 and Cebpd and epigenetically repressed their transcription. Collectively, this study reveals CUL4B-mediated epigenetic regulation of the osteogenic or adipogenic commitment of MSCs, which has therapeutic implications in osteoporosis.
Multi-cancer analysis reveals universal association of oncogenic LBH expression with DNA hypomethylation and WNT-Integrin signaling pathways
Authors: Young In-Chi , Brabletz Thomas , Lindley Linsey E. , Abreu Maria , Nagathihalli Nagaraj , Zaika Alexander , Briegel Karoline J. 
Published: June 2023

AbstractLimb-Bud and Heart (LBH) is a developmental transcription co-factor deregulated in cancer, with reported oncogenic and tumor suppressive effects. However, LBH expression in most cancer types remains unknown, impeding understanding of its mechanistic function Here, we performed systematic bioinformatic and TMA analysis for LBH in >20 different cancer types. LBH was overexpressed in most cancers compared to normal tissues (>1.5-fold; p < 0.05), including colon-rectal, pancreatic, esophageal, liver, stomach, bladder, kidney, prostate, testicular, brain, head & neck cancers, and sarcoma, correlating with poor prognosis. The cancer types showing LBH downregulation were lung, melanoma, ovarian, cervical, and uterine cancer, while both LBH over- and under-expression were observed in hematopoietic malignancies. In cancers with LBH overexpression, the LBH locus was frequently hypomethylated, identifying DNA hypomethylation as a potential mechanism for LBH dysregulation. Pathway analysis identified a universal, prognostically significant correlation between LBH overexpression and the WNT-Integrin signaling pathways. Validation of the clinical association of LBH with WNT activation in gastrointestinal cancer cell lines, and in colorectal patient samples by IHC uncovered that LBH is specifically expressed in tumor cells with nuclear beta-catenin at the invasive front. Collectively, these data reveal a high degree of LBH dysregulation in cancer and establish LBH as pan-cancer biomarker for detecting WNT hyperactivation in clinical specimens.
Comparison of repeat penetrating keratoplasty, DSAEK and DMEK for the management of endothelial failure of previous PK
Authors: Roberts Harry W. , de Benito-Llopis Laura 
Published: June 2023

Abstract
Purpose
To compare the clinical outcomes of repeat PK, DSAEK-on-PK or DMEK-on-PK for the management of endothelial failure of previous penetrating keratoplasty.

Design
Retrospective, interventional consecutive case series.

Participants
104 consecutive eyes of 100 patients requiring a second keratoplasty for endothelial failure of their primary penetrating keratoplasty performed between September 2016 and December 2020.

Intervention
Repeat keratoplasty.

Main outcome measures
Survival and visual acuity at 12 and 24 months, rebubbling rate and complications.

Results
Repeat PK was performed in 61/104 eyes (58.7%), DSAEK-on-PK was performed in 21/104 eyes (20.2%) and DMEK-on-PK was performed in 22/104 eyes (21.2%). Failure rates in the first 12 and 24 months were 6.6% and 20.6% for repeat PKs compared to 19% and 30.6% for DSAEK and 36.4% and 41.3% for DMEK. For those grafts surviving 12 months, the chances of surviving to 24 months were greatest for DMEK-on-PK at 92% vs 85% each for redo PK and DSAEK-on-PK. Visual acuity at one year was logMAR 0.53 ± 0.51 in the redo PK group, 0.25 ± 0.17 for DSAEK-on-PK and 0.30 ± 0.38 for DMEK-on-PK. 24-month outcomes were 0.34 ± 0.28, 0.08 ± 0.16, and 0.36 ± 0.36 respectively.

Conclusions
DMEK-on-PK has a greater failure rate in the first 12 months than DSAEK-on-PK which has a greater failure rate than redo PK. However, the 2-year survival rates in our series for those already surviving 12 months were greatest for DMEK-on-PK. There was no significant difference in visual acuity at 12 or 24 months. Careful patient selection is needed by experienced surgeons to determine which procedure to offer to patients.
Unique Huygens-Fresnel electromagnetic transportation of chiral Dirac wavelet in topological photonic crystal
Authors: Wang Xing-Xiang , Guo Zhiwei , Song Juan , Jiang Haitao , Chen Hong , Hu Xiao 
Published: June 2023

AbstractLight propagates in various ways depending on environment, including uniform medium, surface/interface and photonic crystals, which appears ubiquitously in daily life and has been exploited for advanced optics technology. We unveiled that a topological photonic crystal exhibits unique electromagnetic (EM) transport properties originating from the Dirac frequency dispersion and multicomponent spinor eigenmodes. Measuring precisely local Poynting vectors in microstrips of honeycomb structure where optics topology emerges upon a band gap opening in the Dirac dispersion and a p-d band inversion induced by a Kekulé-type distortion respecting C6v symmetry, we showed that a chiral wavelet induces a global EM transportation circulating in the direction counter to the source, which is intimately related to the topological band gap specified by a negative Dirac mass. This brand-new Huygens-Fresnel phenomenon can be considered as the counterpart of negative refraction of EM plane waves associated with upwardly convex dispersions of photonic crystals, and our present finding is expected to open a new window for photonic innovations.
Cryogenic characteristics of graphene composites—evolution from thermal conductors to thermal insulators
Authors: Nataj Zahra Ebrahim , Xu Youming , Wright Dylan , Brown Jonas O. , Garg Jivtesh , Chen Xi , Kargar Fariborz , Balandin Alexander A. 
Published: June 2023

AbstractThe development of cryogenic semiconductor electronics and superconducting quantum computing requires composite materials that can provide both thermal conduction and thermal insulation. We demonstrated that at cryogenic temperatures, the thermal conductivity of graphene composites can be both higher and lower than that of the reference pristine epoxy, depending on the graphene filler loading and temperature. There exists a well-defined cross-over temperature—above it, the thermal conductivity of composites increases with the addition of graphene; below it, the thermal conductivity decreases with the addition of graphene. The counter-intuitive trend was explained by the specificity of heat conduction at low temperatures: graphene fillers can serve as, both, the scattering centers for phonons in the matrix material and as the conduits of heat. We offer a physical model that explains the experimental trends by the increasing effect of the thermal boundary resistance at cryogenic temperatures and the anomalous thermal percolation threshold, which becomes temperature dependent. The obtained results suggest the possibility of using graphene composites for, both, removing the heat and thermally insulating components at cryogenic temperatures—a capability important for quantum computing and cryogenically cooled conventional electronics.
Serine ADP-ribosylation in Drosophila provides insights into the evolution of reversible ADP-ribosylation signalling
Authors: Fontana Pietro , Buch-Larsen Sara C. , Suyari Osamu , Smith Rebecca , Suskiewicz Marcin J. , Schützenhofer Kira , Ariza Antonio , Rack Johannes Gregor Matthias , Nielsen Michael L. , Ahel Ivan 
Published: June 2023

AbstractIn the mammalian DNA damage response, ADP-ribosylation signalling is of crucial importance to mark sites of DNA damage as well as recruit and regulate repairs factors. Specifically, the PARP1:HPF1 complex recognises damaged DNA and catalyses the formation of serine-linked ADP-ribosylation marks (mono-Ser-ADPr), which are extended into ADP-ribose polymers (poly-Ser-ADPr) by PARP1 alone. Poly-Ser-ADPr is reversed by PARG, while the terminal mono-Ser-ADPr is removed by ARH3. Despite its significance and apparent evolutionary conservation, little is known about ADP-ribosylation signalling in non-mammalian Animalia. The presence of HPF1, but absence of ARH3, in some insect genomes, including Drosophila species, raises questions regarding the existence and reversal of serine-ADP-ribosylation in these species. Here we show by quantitative proteomics that Ser-ADPr is the major form of ADP-ribosylation in the DNA damage response of Drosophila melanogaster and is dependent on the dParp1:dHpf1 complex. Moreover, our structural and biochemical investigations uncover the mechanism of mono-Ser-ADPr removal by Drosophila Parg. Collectively, our data reveal PARP:HPF1-mediated Ser-ADPr as a defining feature of the DDR in Animalia. The striking conservation within this kingdom suggests that organisms that carry only a core set of ADP-ribosyl metabolising enzymes, such as Drosophila, are valuable model organisms to study the physiological role of Ser-ADPr signalling.
Evaluating the use of blood pressure polygenic risk scores across race/ethnic background groups
Authors: Kurniansyah Nuzulul , Goodman Matthew O. , Khan Alyna T. , Wang Jiongming , Feofanova Elena , Bis Joshua C. , Wiggins Kerri L. , Huffman Jennifer E. , Kelly Tanika , Elfassy Tali , Guo Xiuqing , Palmas Walter , Lin Henry J. , Hwang Shih-Jen , Gao Yan , Young Kendra , Kinney Gregory L. , Smith Jennifer A. , Yu Bing , Liu Simin , Wassertheil-Smoller Sylvia , Manson JoAnn E. , Zhu Xiaofeng , Chen Yii-Der Ida , Lee I-Te , Gu C. Charles , Lloyd-Jones Donald M. , Zöllner Sebastian , Fornage Myriam , Kooperberg Charles , Correa Adolfo , Psaty Bruce M. , Arnett Donna K. , Isasi Carmen R. , Rich Stephen S. , Kaplan Robert C. , Redline Susan , Mitchell Braxton D. , Franceschini Nora , Levy Daniel , Rotter Jerome I. , Morrison Alanna C. , Sofer Tamar 
Published: June 2023

AbstractWe assess performance and limitations of polygenic risk scores (PRSs) for multiple blood pressure (BP) phenotypes in diverse population groups. We compare “clumping-and-thresholding” (PRSice2) and LD-based (LDPred2) methods to construct PRSs from each of multiple GWAS, as well as multi-PRS approaches that sum PRSs with and without weights, including PRS-CSx. We use datasets from the MGB Biobank, TOPMed study, UK biobank, and from All of Us to train, assess, and validate PRSs in groups defined by self-reported race/ethnic background (Asian, Black, Hispanic/Latino, and White). For both SBP and DBP, the PRS-CSx based PRS, constructed as a weighted sum of PRSs developed from multiple independent GWAS, perform best across all race/ethnic backgrounds. Stratified analysis in All of Us shows that PRSs are better predictive of BP in females compared to males, individuals without obesity, and middle-aged (40-60 years) compared to older and younger individuals.
Light-switchable transcription factors obtained by direct screening in mammalian cells
Authors: Zhu Liyuan , McNamara Harold M. , Toettcher Jared E. 
Published: June 2023

AbstractOptogenetic tools can provide fine spatial and temporal control over many biological processes. Yet the development of new light-switchable protein variants remains challenging, and the field still lacks general approaches to engineering or discovering protein variants with light-switchable biological functions. Here, we adapt strategies for protein domain insertion and mammalian-cell expression to generate and screen a library of candidate optogenetic tools directly in mammalian cells. The approach is based on insertion of the AsLOV2 photoswitchable domain at all possible positions in a candidate protein of interest, introduction of the library into mammalian cells, and light/dark selection for variants with photoswitchable activity. We demonstrate the approach’s utility using the Gal4-VP64 transcription factor as a model system. Our resulting LightsOut transcription factor exhibits a > 150-fold change in transcriptional activity between dark and blue light conditions. We show that light-switchable function generalizes to analogous insertion sites in two additional Cys6Zn2 and C2H2 zinc finger domains, providing a starting point for optogenetic regulation of a broad class of transcription factors. Our approach can streamline the identification of single-protein optogenetic switches, particularly in cases where structural or biochemical knowledge is limited.
Antiviral effect of SARS-CoV-2 N-specific CD8+ T cells induced in lungs by engineered extracellular vesicles
Authors: Manfredi Francesco , Chiozzini Chiara , Ferrantelli Flavia , Leone Patrizia , Pugliese Katherina , Spada Massimo , Di Virgilio Antonio , Giovannelli Andrea , Valeri Mauro , Cara Andrea , Michelini Zuleika , Andreotti Mauro , Federico Maurizio 
Published: June 2023

AbstractInduction of effective immunity in the lungs should be a requisite for any vaccine designed to control the severe pathogenic effects generated by respiratory infectious agents. We recently provided evidence that the generation of endogenous extracellular vesicles (EVs) engineered for the incorporation of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV)-2 Nucleocapsid (N) protein induced immunity in the lungs of K18-hACE2 transgenic mice, which then can survive the lethal virus infection. However, nothing is known about the ability of the N-specific CD8+ T cell immunity in controlling viral replication in the lungs, a major pathogenic signature of severe disease in humans. To fill the gap, we investigated the immunity generated in the lungs by N-engineered EVs in terms of induction of N-specific effectors and resident memory CD8+ T lymphocytes before and after virus challenge carried out three weeks and three months after boosting. At the same time points, viral replication extents in the lungs were evaluated. Three weeks after the second immunization, virus replication was reduced in mice best responding to vaccination by more than 3-logs compared to the control group. The impaired viral replication matched with a reduced induction of Spike-specific CD8+ T lymphocytes. The antiviral effect appeared similarly strong when the viral challenge was carried out 3 months after boosting, and associated with the persistence of N-specific CD8+ T-resident memory lymphocytes. In view of the quite low mutation rate of the N protein, the present vaccine strategy has the potential to control the replication of all emerging variants.
An EEG database for the cognitive assessment of motor imagery during walking with a lower-limb exoskeleton
Authors: Ortiz Mario , de la Ossa Luis , Juan Javier , Iáñez Eduardo , Torricelli Diego , Tornero Jesús , Azorín José M. 
Published: June 2023

AbstractOne important point in the development of a brain-machine Interface (BMI) commanding an exoskeleton is the assessment of the cognitive engagement of the subject during the motor imagery tasks conducted. However, there are not many databases that provide electroencephalography (EEG) data during the use of a lower-limb exoskeleton. The current paper presents a database designed with an experimental protocol aiming to assess not only motor imagery during the control of the device, but also the attention to gait on flat and inclined surfaces. The research was conducted as an EUROBENCH subproject in the facilities sited in Hospital Los Madroños, Brunete (Madrid). The data validation reaches accuracies over 70% in the assessment of motor imagery and attention to gait, which marks the present database as a valuable resource for researches interested on developing and testing new EEG-based BMIs.