bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rheology of the Fluid Oversaturated Fault Zones at the Brittle‐Plastic Transition
Authors: Okazaki Keishi , Burdette Eric , Hirth Greg 
Published: January 2021

AbstractLarge earthquakes and slow slip events typically nucleate along plate boundaries near the depth limit of the seismogenic zone, which is also recognized as the brittle‐plastic transition zone (BPT). High Vp/Vs ratios are commonly observed at the BPT in subduction zones, indicating the presence of aqueous fluid in pore spaces. We conducted experiments to investigate the rheology of quartz with different fluid fractions at deformation conditions that cross the BPT. The strengths of quartz aggregates with fluid‐filled porosities of 5–25 vol% are significantly lower than predicted by wet quartzite flow laws, and decrease with increasing fluid fraction. Recovered samples deformed in the ductile regime exhibit S‐C´ mylonitic structures characterized by elongate grains, shear localization and fluid segregation. Variations in strength are explained by a combination of a constitutive law for dislocation creep that includes the geometric effects of fluid fraction, a friction law that includes the effect of fluid fraction through its role on the real area of contact, and an empirical function to describe the smooth brittle‐plastic transition. Our results indicate that the presence of fluid‐filled porosity promotes significant weakening in shear zones, and that variations in fluid fraction (together with temperature) can explain transitions in the spectrum of slip behaviors observed along plate boundaries.
Wintertime Formaldehyde: Airborne Observations and Source Apportionment Over the Eastern United States
Authors: Green Jaime R. , Fiddler Marc N. , Fibiger Dorothy L. , McDuffie Erin E. , Aquino Janine , Campos Teresa , Shah Viral , Jaeglé Lyatt , Thornton Joel A. , DiGangi Joshua P. , Wolfe Glenn M. , Bililign Solomon , Brown Steven S. 
Published: January 2021

AbstractFormaldehyde (HCHO) is generated from direct urban emission sources and secondary production from the photochemical reactions of urban smog. HCHO is linked to tropospheric ozone formation, and contributes to the photochemical reactions of other components of urban smog. In this study, pollution plume intercepts during the Wintertime INvestigation of Transport, Emissions, and Reactivity (WINTER) campaign were used to investigate and characterize the formation of HCHO in relation to several anthropogenic tracers. Analysis of aircraft intercepts combined with detailed chemical box modeling downwind of several cities suggests that the most important contribution to observed HCHO was primary emission. A box model analysis of a single plume suggested that secondary sources contribute to 21 ± 10% of the observed HCHO. Ratios of HCHO/CO observed in the northeast US, from Ohio to New York, ranging from 0.2% to 0.6%, are consistent with direct emissions combined with at most modest photochemical production. Analysis of the nocturnal boundary layer and residual layer from repeated vertical profiling over urban influenced areas indicate a direct HCHO emission flux of 1.3 × 1014 molecules cm−2 h−1. In a case study in Atlanta, GA, nighttime HCHO exhibited a ratio to CO (0.6%–1.8%) and was anti‐correlated with O3. Observations were consistent with mixing between direct HCHO emissions in urban air masses with those influenced by more rapid HCHO photochemical production. The HCHO/CO emissions ratios determined from the measured data are 2.3–15 times greater than the NEI 2017 emissions database. The largest observed HCHO/CO was 1.7%–1.8%, located near co‐generating power stations.
Seismic Ambient Noise Analyses Reveal Changing Temperature and Water Signals to 10s of Meters Depth in the Critical Zone
Authors: Oakley David O. S. , Forsythe Brandon , Gu Xin , Nyblade Andrew A. , Brantley Susan L. 
Published: January 2021

AbstractThe critical zone sustains terrestrial life, but we have few tools to explore it efficiently beyond the first few meters of the subsurface. Using analyses of high‐frequency ambient seismic noise from densely spaced seismometers deployed in the forested Shale Hills subcatchment of the Susquehanna Shale Hills Critical Zone Observatory (SSHCZO), we show that temporal changes in seismic velocities at depths from ∼1 m to tens of m can be detected. These changes are driven by variations at the land surface. The Moving‐Window Cross‐Spectral (MWCS) method was employed to measure seismic‐velocity changes in coda waves at hourly resolution in 10 different frequency bands. We observed a diurnal signal, a seasonal signal, and a meteorological‐event‐based signal. These signals were compared to time‐series measurements of precipitation, well water levels, soil moisture, soil temperature, air temperature, latent heat flux, and air pressure in the heavily instrumented catchment. Most of the velocity changes can be explained by variations in temperature that result in thermoelastic strains that propagate to depth. But some double minima in seismic velocity time‐series observed after large rain events were attributed in part to the effects of water infiltration. These results show that high‐frequency ambient noise data may in some locations be used to detect changes in the critical zone from ∼1 to ∼100 m or greater depth with hourly resolution. But interpretation of such data requires multiple environmental data sets to deconvolve the complex interrelationships among thermoelastic and hydrological effects in the subsurface critical zone.
Ground‐Based GNSS and C/NOFS Observations of Ionospheric Irregularities Over Africa: A Case Study of the 2013 St. Patrick’s Day Geomagnetic Storm
Authors: Amaechi P. O. , Oyeyemi E. O. , Akala A. O. , Messanga H. E. , Panda S. K. , Seemala Gopi K. , Oyedokun J. O. , Fleury R. , Amory‐Mazaudier C. 
Published: January 2021

AbstractIn this paper, the variations of ionospheric irregularities have been studied using C/NOFS, ground‐based GNSS and magnetometer measurements in Africa during the St. Patrick geomagnetic storm of March 17, 2013. The latitudinal distribution of irregularities was examined using GNSS‐ROTI maps covering longitude 25°–45°E. Longitudinal characteristics were also investigated along with equatorial plasma bubbles (EPBs) and vertical drift velocity (Vz) from 12 to 21 March 2013. The results show postsunset irregularities from 12°S–27°N with the stronger ones confined within 1°S–7°S and 12°N–22°N in the prestorm period. The observed pre‐reversal enhancement (PRE) with Vz varying from 22.51–59.47 m/s between 20.26 and 20.86 LT corresponded with the occurrence of EPBs. PRE greater than 40 m/s nevertheless, supported long lasting depletions. During the main phase, prompt penetration electric field enhanced the PRE thus, extended the latitudinal range of irregularities to 31°N. It also induced a long duration EPB along 15°E and several depletions over the Eastern sector. During the recovery phase, stormtime wind drove a conspicuous asymmetry in the morphology of the postsunset anomaly. This corresponded with the reduction in the latitudinal extent and strength of irregularities. Westward/eastward disturbance dynamo electric field inhibited/triggered irregularities in the postsunset/postmidnight period on 18 March over the Eastern sector. The difference in the drift accounted for the longitudinal variations of irregularities before the storm. During the main phase however, irregularities were present (reduced) over the Eastern (Atlantic/Western) sectors. This difference might have been related to the changes in the wind inferred from the anomaly shape.
Comment on ‘‘A Modular Framework for Modeling Unsaturated Soil Hydraulic Properties Over the Full Moisture Range” by Weber et al.
Authors: Peters Andre , Iden Sascha C. 
Published: January 2021

AbstractWeber et al. (2019) (W19 in the following) present a modular framework for parametrizing soil hydraulic properties. The W19 model framework is almost identical to the model system developed jointly by Peters (2013), https://doi.org/10.1002/wrcr.20548, Iden and Durner (2014), https://doi.org/10.1002/2014wr015937, and Peters (2014), https://doi.org/10.1002/2014wr016107, to which we will refer as PDI ("Peters‐Durner‐Iden") model in the following. The primary goal of this comment is to uncover some inconsistencies of the W19 formulation. In the following, we (i) comment on the statement made by W19 regarding the number of parameters in the original PDI formulation, (ii) critically analyze the use of their function to parameterize the water retention curve (WRC), and (iii) show that, in contrast to the statement in W19, using their formulation of for parametrizing noncapillary hydraulic conductivity leads to systematic deviations from the physically based film‐conductivity model developed by Tokunaga (2009), https://doi.org/10.1029/2009wr007734.
Secretoglobin 3A2 eliminates human cancer cells through pyroptosis
Authors: Yokoyama Shigetoshi , Nakayama Shun , Xu Lei , Pilon Aprile L. , Kimura Shioko 
Published: January 2021

AbstractNon-canonical inflammasome activation that recognizes intracellular lipopolysaccharide (LPS) causes pyroptosis, the inflammatory death of innate immune cells. The role of pyroptosis in innate immune cells is to rapidly eliminate pathogen-infected cells and limit the replication niche in the host body. Whether this rapid cell elimination process of pyroptosis plays a role in elimination of cancer cells is largely unknown. Our earlier study demonstrated that a multi-functional secreted protein, secretoglobin (SCGB) 3A2, chaperones LPS to cytosol, and activates caspase-11 and the non-canonical inflammasome pathway, leading to pyroptosis. Here we show that SCGB3A2 exhibits marked anti-cancer activity against 5 out of 11 of human non-small cell lung cancer cell lines in mouse xenographs, while no effect was observed in 6 of 6 small cell lung cancer cell lines examined. All SCGB3A2-LPS-sensitive cells express syndecan 1 (SDC1), a SCGB3A2 cell surface receptor, and caspase-4 (CASP4), a critical component of the non-canonical inflammasome pathway. Two epithelial-derived colon cancer cell lines expressing SDC1 and CASP4 were also susceptible to SCGB3A2-LPS treatment. TCGA analysis revealed that lung adenocarcinoma patients with higherSCGB3A2mRNA levels exhibited better survival. These data suggest that SCGB3A2 uses the machinery of pyroptosis for the elimination of human cancer cells via the non-canonical inflammasome pathway, and that SCGB3A2 may serve as a novel therapeutic to treat cancer, perhaps in combination with immuno and/or targeted therapies.
A catalogue of 863 Rett-syndrome-causing MECP2 mutations and lessons learned from data integration
Authors: Ehrhart Friederike , Jacobsen Annika , Rigau Maria , Bosio Mattia , Kaliyaperumal Rajaram , Laros Jeroen F. J. , Willighagen Egon L. , Valencia Alfonso , Roos Marco , Capella-Gutierrez Salvador , Curfs Leopold M. G. , Evelo Chris T. 
Published: January 2021

AbstractRett syndrome (RTT) is a rare neurological disorder mostly caused by a genetic variation in MECP2. Making new MECP2 variants and the related phenotypes available provides data for better understanding of disease mechanisms and faster identification of variants for diagnosis. This is, however, currently hampered by the lack of interoperability between genotype-phenotype databases. Here, we demonstrate on the example of MECP2 in RTT that by making the genotype-phenotype data more Findable, Accessible, Interoperable, and Reusable (FAIR), we can facilitate prioritization and analysis of variants. In total, 10,968 MECP2 variants were successfully integrated. Among these variants 863 unique confirmed RTT causing and 209 unique confirmed benign variants were found. This dataset was used for comparison of pathogenicity predicting tools, protein consequences, and identification of ambiguous variants. Prediction tools generally recognised the RTT causing and benign variants, however, there was a broad range of overlap Nineteen variants were identified that were annotated as both disease-causing and benign, suggesting that there are additional factors in these cases contributing to disease development.
Probing the role of thermal vibrational disorder in the SPT of VO$$_2$$ by Raman spectroscopy
Authors: Suleiman Aminat Oyiza , Mansouri Sabeur , Émond Nicolas , Le Drogoff Boris , Bégin Théophile , Margot Joëlle , Chaker Mohamed 
Published: January 2021

AbstractPhase competition in transition metal oxides has attracted remarkable interest for fundamental aspects and technological applications. Here, we report a concurrent study of the phase transitions in undoped and Cr-doped VO$$_2$$

2

thin films. The structural, morphological and electrical properties of our films are examined and the microstructural effect on the metal–insulator transition (MIT) are highlighted. We further present a distinctive approach for analyzing the Raman data of undoped and Cr-doped VO$$_2$$

2

thin films as a function of temperature, which are quantitatively correlated to the electrical measurements of VO$$_2$$

2

films to give an insight into the coupling between the structural phase transition (SPT) and the MIT. These data are also combined with reported EXAFS measurements and a connection between the Raman intensities and the mean Debye–Waller factors $$\sigma ^2$$

σ
2

is established. We found that the temperature dependence of the $$\sigma _{R}^{2}(V-V)$$

σ

R

2

(
V
-
V
)

as calculated from the Raman intensity retraces the temperature profile of the $$\sigma _{EXAFS}^{2}(V-V)$$

σ

EXAFS

2

(
V
-
V
)

as obtained from the EXAFS data analysis. Our findings provide an evidence on the critical role of the thermal vibrational disorder in the VO$$_2$$

2

phase transitions. Our study demonstrates that correlating Raman data with EXAFS analysis, the lattice and electronic structural dynamics can be probed.
Primary Sjogren syndrome increases the risk of bisphosphonate-related osteonecrosis of the jaw
Authors: Kuo Pei-I , Lin Tzu-Min , Chang Yu-Sheng , Hou Tsung-Yun , Hsu Hui-Ching , Lin Sheng-Hong , Chen Wei-Sheng , Lin Yi-Chun , Wang Li-Hsuan , Chang Chi-Ching , Chen Jin-Hua 
Published: January 2021

AbstractThe risk of bisphosphonate-related osteonecrosis of the jaw (BRONJ) in primary Sjogren syndrome (pSS) has rarely been explored. To explore the association between BRONJ and pSS, we conducted a population-based propensity-score-matched cohort study using Taiwan’s National Health Insurance Research Database, including pSS patients receiving antiosteoporotic therapy and patients without pSS receiving antiosteoporotic therapy. A 1:4 matched-pair cohort based on propensity score was created. The stratified Cox proportional hazards model compared the risk of BRONJ in the pSS and non-pSS groups. In the study, 23,280 pSS patients and 28,712,152 controls were enrolled. After matching, 348 patients with pSS receiving antiosteoporotic drugs and 50,145 without pSS receiving antiosteoporotic drugs were included for analysis. The risk of developing BRONJ was 1.96 times higher in pSS patients compared with non-pSS patients after adjustment for age, sex, and comorbidities. No dose–response effect was observed in the bisphosphonate-treated pSS cohorts, documented as the cumulative defined daily doses of either < 224 or ≥ 224 (hazard ratio [HR]: 2.407, 95% confidence interval [CI] 1.412–7.790; HR: 2.143, 95% CI 1.046–4.393, respectively) increased risk of developing osteonecrosis of the jaw. In conclusion, the risk of BRONJ is significantly higher in patients with pSS compared with the general population.
Weighted gene co-expression network analysis of the salt-responsive transcriptomes reveals novel hub genes in green halophytic microalgae Dunaliella salina
Authors: Panahi Bahman , Hejazi Mohammad Amin 
Published: January 2021

AbstractDespite responses to salinity stress in Dunaliella salina, a unicellular halotolerant green alga, being subject to extensive study, but the underlying molecular mechanism remains unknown. Here, Empirical Bayes method was applied to identify the common differentially expressed genes (DEGs) between hypersaline and normal conditions. Then, using weighted gene co-expression network analysis (WGCNA), which takes advantage of a graph theoretical approach, highly correlated genes were clustered as a module. Subsequently, connectivity patterns of the identified modules in two conditions were surveyed to define preserved and non-preserved modules by combining the Zsummary and medianRank measures. Finally, common and specific hub genes in non-preserved modules were determined using Eigengene-based module connectivity or module membership (kME) measures and validation was performed by using leave-one-out cross-validation (LOOCV). In this study, the power of beta = 12 (scale-free R2 = 0.8) was selected as the soft-thresholding to ensure a scale-free network, which led to the identification of 15 co-expression modules. Results also indicate that green, blue, brown, and yellow modules are non-preserved in salinity stress conditions. Examples of enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways in non-preserved modules are Sulfur metabolism, Oxidative phosphorylation, Porphyrin and chlorophyll metabolism, Vitamin B6 metabolism. Moreover, the systems biology approach was applied here, proposed some salinity specific hub genes, such as radical-induced cell death1 protein (RCD1), mitogen-activated protein kinase kinase kinase 13 (MAP3K13), long-chain acyl-CoA synthetase (ACSL), acetyl-CoA carboxylase, biotin carboxylase subunit (AccC), and fructose-bisphosphate aldolase (ALDO), for the development of metabolites accumulating strains in D. salina.
EBF1 drives hallmark B cell gene expression by enabling the interaction of PAX5 with the MLL H3K4 methyltransferase complex
Authors: Bullerwell Charles E. , Robichaud Philippe Pierre , Deprez Pierre M. L. , Joy Andrew P. , Wajnberg Gabriel , D’Souza Darwin , Chacko Simi , Fournier Sébastien , Crapoulet Nicolas , Barnett David A. , Lewis Stephen M. , Ouellette Rodney J. 
Published: January 2021

AbstractPAX5 and EBF1 work synergistically to regulate genes that are involved in B lymphocyte differentiation. We used the KIS-1 diffuse large B cell lymphoma cell line, which is reported to have elevated levels of PAX5 expression, to investigate the mechanism of EBF1- and PAX5-regulated gene expression. We demonstrate the lack of expression of hallmark B cell genes, including CD19, CD79b, and EBF1, in the KIS-1 cell line. Upon restoration of EBF1 expression we observed activation of CD19, CD79b and other genes with critical roles in B cell differentiation. Mass spectrometry analyses of proteins co-immunoprecipitated with PAX5 in KIS-1 identified components of the MLL H3K4 methylation complex, which drives histone modifications associated with transcription activation. Immunoblotting showed a stronger association of this complex with PAX5 in the presence of EBF1. Silencing of KMT2A, the catalytic component of MLL, repressed the ability of exogenous EBF1 to activate transcription of both CD19 and CD79b in KIS-1 cells. We also find association of PAX5 with the MLL complex and decreased CD19 expression following silencing of KMT2A in other human B cell lines. These data support an important role for the MLL complex in PAX5-mediated transcription regulation.
Effect of volatile and total intravenous anesthesia on syndecan-1 shedding after minimally invasive gastrectomy: a randomized trial
Authors: Kim Na Young , Kim Ki Jun , Lee Ki-Young , Shin Hye Jung , Cho Jaein , Nam Da Jeong , Kim So Yeon 
Published: January 2021

AbstractThis study aimed to compare the effects of volatile anesthesia and total intravenous anesthesia (TIVA) on syndecan-1 shedding in patients with gastric cancer undergoing minimally invasive gastrectomy. Patients were randomly assigned to either the Volatile (n = 68) or the TIVA (n = 68) group. Anesthesia was maintained with sevoflurane/remifentanil or propofol/remifentanil in the Volatile and TIVA groups, respectively. Serum syndecan-1 was evaluated at pre-operation, end of operation, and postoperative day (POD) 1. Inflammatory markers including white blood cell (WBC) count, neutrophil-to-lymphocyte ratio (NLR), and C-reactive protein (CRP), were also measured at pre-operation, end of operation, and POD 1, 2, 3, and 5. The TIVA group showed significantly lower levels of syndecan-1 at the end of the operation compared to the Volatile group; however, no difference was seen between the groups at POD 1. The WBC count and NLR were significantly lower in the TIVA group at the end of the operation than the Volatile group, but there were no differences between the groups at POD 1, 2, 3, and 5. CRP levels were similar between the groups at all time points. In conclusion, despite TIVA being superior to volatile anesthesia in protecting endothelial glycocalyx during the operation, both did not prevent postoperative syndecan-1 shedding after gastrectomy.Clinical trial registration number: NCT04183296 (ClinicalTrial.gov, 03/12/2019).
Nonconventional driving force for selective oxidative C–C coupling reaction due to concurrent and curious formation of Ag0
Authors: Bhanderi Khushboo , Ghalsasi Prasanna S. , Inoue Katsuya 
Published: January 2021

AbstractIs it possible to ‘explore’ metal’s intrinsic property—a cohesive interaction—which naturally transform M0 into an aggregate or a particle or film for driving oxidative C–C bond formation? With this intention, reduction of [Ag(NH3)2]+ to Ag0 with concurrent oxidation of different phenols/naphthols to biphenyls was undertaken. The work is originated during careful observation of an undergraduate experiment—Tollens’ test—where silver mirror film deposition takes place on the walls of borosilicate glass test tube. When the same reaction was carried out in polypropylene (plastic-Eppendorf) tube, we observed aggregation of Ag0 leading to floating Ag-particles but not silver film deposition. This prompted us to carry out challenging cross-coupling reaction by ONLY changing the surface of the reaction flask from glass to plastic to silicones. To our surprise, we observed good selective oxidative homo-coupling on Teflon surface while cross-coupling in Eppendorf vial. Thus, we propose that the formation of biphenyl is driven by the macroscopic growth of Ag0 into [Ag-particle] orchestrated by Ag…Ag cohesive interaction. To validate results, experiments were also performed on gram scale. More importantly, oxidation of β-naphthol carried out in quartz (chiral) tube which yielded slight enantioselective excess of BINOL. Details are discussed.