bluuebunny/crossref_metadata_2025_split huggingface dataset:
Time Dependent Mechanical Crack Closure as a Potential Rapid Source of Post‐Seismic Wave Speed Recovery: Insights From Experiments in Carrara Marble
Authors: Meyer Gabriel G. , Brantut Nicolas , Mitchell Thomas M. , Meredith Philip G. , Plümper Oliver 
Published: March 2021

AbstractSeismological observations indicate strong variations in wave velocities around faults both co‐seismically during earthquakes, and post‐seismically. Recovery is commonly associated with a reduction in crack damage. Here, we explore the recovery associated with time‐dependent mechanical closure of cracks. We report results from laboratory experiments conducted on dry cores of Carrara marble at room temperature. We deformed cylindrical samples in the semi‐brittle regime to induce crack damage before subjecting them to hydrostatic and triaxial stress conditions for extended periods of time while recording dilatancy and wave speeds repeatedly. We report wave speed increases of up to 40% of the damage‐induced wave speed drop in samples subject to hydrostatic loading. Moreover, we report the occurrence of significant wave speed increases contemporaneously with time‐dependent creep in triaxially loaded samples. Wave speed recovery during creep is only observed below a threshold creep strain rate, a result we interpret as a transition from brittle to plastic creep with decreasing strain rate. We interpret the wave speed increase in terms of reduced crack density and increased contact area within the crack array, and show that around 40% of the total crack surface has to be closed to justify the observed wave speed recoveries. We propose that mechanical crack closure is driven by the viscous relaxation of the bulk rock under the influence of locked‐in stresses at low confining pressure, and of the external stresses at higher confining pressure. Our study shows that mechanical crack closure is a significant source of time‐dependent wave speed recovery.
Three‐Dimensional Simulation of Shoaling Internal Solitary Waves and Their Influence on Particle Transport in the Southern Red Sea
Authors: Guo Daquan , Zhan Peng , Hoteit Ibrahim 
Published: March 2021

AbstractThe shoaling process of a group of internal solitary waves (ISWs) in the southern Red Sea is simulated with a three dimensional, nonhydrostatic, high‐resolution MIT general circulation model. The breaking and dissipation processes are well reproduced, in which a positive tail forms behind and locally moves the interface upward, causing the transformation of wave polarity as it moves onshore. With the step‐like structure followed, the wave eventually evolves into smaller water bores. Combined with the parameters of the leading wave slope (Sw) of about 0.07 and topography slope (S) of about 0.01, the shoaling is suggested to follow a mild breaking process. The particle transport during the shoaling process is further examined quantitatively using the Connectivity modeling system (CMS). About 38,400 particles are released at six different vertical layers in the main shoaling domain. Most of the particles are transported up‐and‐down following the wave oscillation process then settle within 10–20 m around the original released depth. For the particles inside the breaking area, the oscillation process becomes more complex and intensified, and eventually a great portion of these particles settle far away from their released locations. The time‐integrated transport distance, Ti, and the direct transport distance, Ts, are also analyzed. With Ti almost 20 times to Ts in vertical, continuous up‐and‐down movements are suggested during the shoaling process.
Under Ice and Early Summer Phytoplankton Dynamics in Two Arctic Lakes with Differing DOC
Authors: Hazuková V. , Burpee B. T. , McFarlane‐Wilson I. , Saros J. E. 
Published: March 2021

AbstractWe investigated Arctic lake phytoplankton response along vertical gradients in the water column during seasonal succession from ice‐covered to open‐water conditions. Two oligotrophic lakes in West Greenland with different dissolved organic carbon (DOC) concentrations were selected. We assessed which factors: (1) promote under‐ice growth of phytoplankton, and (2) trigger shifts in the community structure. Our results suggest that DOC is an important driver of the seasonal distribution of phytoplankton biomass—high DOC exacerbates light limitation under ice resulting in low phytoplankton biomass, but supports phytoplankton growth during the open‐water period when photolytic and biological degradation of organic matter contributes to the pool of available nutrients. Under‐ice phytoplankton biomass in a clear, low DOC lake was as high as during the open‐water period, suggesting the importance of under‐ice processes for lake metabolic balance, also evidenced by persistent oxic conditions in the hypolimnion. Species composition was dynamic, reflecting rapidly changing conditions over the course of the season. Our data suggest that phytoplankton under ice provides seed populations for early spring blooms and that the largest shifts in species composition occur later during the summer, likely as a result of nutrient depletion and intensified grazing pressure. Early spring temperatures in West Greenland have risen rapidly in recent decades, triggering shifts in the timing of lake ice‐out and the onset of stratification; therefore, it is important to understand phytoplankton seasonal dynamics to disentangle the effects of climate‐driven shifts on aquatic biota.
Influence of Irrigation Drivers Using Boosted Regression Trees: Kansas High Plains
Authors: Lamb Susan E. , Haacker Erin M. K. , Smidt Samuel J. 
Published: March 2021

AbstractGroundwater levels across parts of western Kansas have been declining at unsustainable rates due to pumping for agricultural irrigation despite water‐saving efforts. Accelerating this decline is the complex agricultural landscape, consisting of both categorical (e.g., management boundaries) and numerical (e.g., crop prices) factors that drive irrigation decisions, making integrated water budget management a challenge. Furthermore, these factors frequently change through time, rendering management strategies outdated within relatively short time scales. This study uses boosted regression trees to simultaneously analyze categorical and numerical data against annual irrigation pumping to determine the relative influence of each factor on groundwater pumping across both space and time. In all, 45 key water use variables covering approximately 19,000 groundwater wells were tested against irrigation pumping from 2006 to 2016 across five categories: (1) management/policy, (2) hydrology, (3) weather, (4) land/agriculture, and (5) economics. Study results showed that variables from all five categories were included among the top 10 drivers to irrigation, and the greatest influence came from variables such as irrigated area per well, saturated thickness, soil permeability, summer precipitation, and pumping costs (depth to water table). Variables that had little influence included regional management boundaries and irrigation technology. The results of this study are further used to target the factors that statistically lead to the greatest volumes of groundwater pumping to help develop robust management strategy suggestions and achieve water management goals of the region.
The AP-1 transcription factors c-Jun and JunB are essential for CD8α conventional dendritic cell identity
Authors: Novoszel Philipp , Drobits Barbara , Holcmann Martin , Fernandes Cristiano De Sa , Tschismarov Roland , Derdak Sophia , Decker Thomas , Wagner Erwin F. , Sibilia Maria 
Published: March 2021

AbstractDendritic cell (DC) development is orchestrated by lineage-determining transcription factors (TFs). Although, members of the activator-protein-1 (AP-1) family, including Batf3, have been implicated in conventional (c)DC specification, the role of Jun proteins is poorly understood. Here, we identified c-Jun and JunB as essential for cDC1 fate specification and function. In mice, Jun proteins regulate extrinsic and intrinsic pathways, which control CD8α cDC1 diversification, whereas CD103 cDC1 development is unaffected. The loss of c-Jun and JunB in DC progenitors diminishes the CD8α cDC1 pool and thus confers resistance to Listeria monocytogenes infection. Their absence in CD8α cDC1 results in impaired TLR triggering and antigen cross-presentation. Both TFs are required for the maintenance of the CD8α cDC1 subset and suppression of cDC2 identity on a transcriptional and phenotypic level. Taken together, these results demonstrate the essential role of c-Jun and JunB in CD8α cDC1 diversification, function, and maintenance of their identity.
Mechanism of substrate transport and inhibition of the human LAT1-4F2hc amino acid transporter
Authors: Yan Renhong , Li Yaning , Müller Jennifer , Zhang Yuanyuan , Singer Simon , Xia Lu , Zhong Xinyue , Gertsch Jürg , Altmann Karl-Heinz , Zhou Qiang 
Published: March 2021

AbstractLAT1 (SLC7A5) is one of the representative light chain proteins of heteromeric amino acid transporters, forming a heterodimer with its heavy chain partner 4F2hc (SLC3A2). LAT1 is overexpressed in many types of tumors and mediates the transfer of drugs and hormones across the blood-brain barrier. Thus, LAT1 is considered as a drug target for cancer treatment and may be exploited for drug delivery into the brain. Here, we synthesized three potent inhibitors of human LAT1, which inhibit transport of leucine with IC50 values between 100 and 250 nM, and solved the cryo-EM structures of the corresponding LAT1-4F2hc complexes with these inhibitors bound at resolution of up to 2.7 or 2.8 Å. The protein assumes an outward-facing occluded conformation, with the inhibitors bound in the classical substrate binding pocket, but with their tails wedged between the substrate binding site and TM10 of LAT1. We also solved the complex structure of LAT1-4F2hc with 3,5-diiodo-l-tyrosine (Diiodo-Tyr) at 3.4 Å overall resolution, which revealed a different inhibition mechanism and might represent an intermediate conformation between the outward-facing occluded state mentioned above and the outward-open state. To our knowledge, this is the first time that the outward-facing conformation is revealed for the HAT family. Our results unveil more important insights into the working mechanisms of HATs and provide a structural basis for future drug design.
WOODIV, a database of occurrences, functional traits, and phylogenetic data for all Euro-Mediterranean trees
Authors: Monnet Anne-Christine , Cilleros Kévin , Médail Frédéric , Albassatneh Marwan Cheikh , Arroyo Juan , Bacchetta Gianluigi , Bagnoli Francesca , Barina Zoltán , Cartereau Manuel , Casajus Nicolas , Dimopoulos Panayotis , Domina Gianniantonio , Doxa Aggeliki , Escudero Marcial , Fady Bruno , Hampe Arndt , Matevski Vlado , Misfud Stephen , Nikolic Toni , Pavon Daniel , Roig Anne , Barea Estefania Santos , Spanu Ilaria , Strid Arne , Vendramin Giovanni Giuseppe , Leriche Agathe 
Published: March 2021

AbstractTrees play a key role in the structure and function of many ecosystems worldwide. In the Mediterranean Basin, forests cover approximately 22% of the total land area hosting a large number of endemics (46 species). Despite its particularities and vulnerability, the biodiversity of Mediterranean trees is not well known at the taxonomic, spatial, functional, and genetic levels required for conservation applications. The WOODIV database fills this gap by providing reliable occurrences, four functional traits (plant height, seed mass, wood density, and specific leaf area), and sequences from three DNA-regions (rbcL,matK, andtrnH-psbA), together with modelled occurrences and a phylogeny for all 210 Euro-Mediterranean tree species. We compiled, homogenized, and verified occurrence data from sparse datasets and collated them on an INSPIRE-compliant 10 × 10 km grid. We also gathered functional trait and genetic data, filling existing gaps where possible. The WOODIV database can benefit macroecological studies in the fields of conservation, biogeography, and community ecology.
Erianthridin suppresses non-small-cell lung cancer cell metastasis through inhibition of Akt/mTOR/p70S6K signaling pathway
Authors: Pothongsrisit Sutthaorn , Arunrungvichian Kuntarat , Hayakawa Yoshihiro , Sritularak Boonchoo , Mangmool Supachoke , Pongrakhananon Varisa 
Published: March 2021

AbstractCancer metastasis is a major cause of the high mortality rate in lung cancer patients. The cytoskeletal rearrangement and degradation of extracellular matrix are required to facilitate cell migration and invasion and the suppression of these behaviors is an intriguing approach to minimize cancer metastasis. Even though Erianthridin (ETD), a phenolic compound isolated from the Thai orchidDendrobium formosumexhibits various biological activities, the molecular mechanism of ETD for anti-cancer activity is unclear. In this study, we found that noncytotoxic concentrations of ETD (≤ 50 μM) were able to significantly inhibit cell migration and invasion via disruption of actin stress fibers and lamellipodia formation. The expression of matrix metalloproteinase-2 (MMP-2) and MMP-9 was markedly downregulated in a dose-dependent manner after ETD treatment. Mechanistic studies revealed that protein kinase B (Akt) and its downstream effectors mammalian target of rapamycin (mTOR) and p70 S6 kinase (p70S6K) were strongly attenuated. An in silico study further demonstrated that ETD binds to the protein kinase domain of Akt with both hydrogen bonding and van der Waals interactions. In addition, an in vivo tail vein injection metastasis study demonstrated a significant effect of ETD on the suppression of lung cancer cell metastasis. This study provides preclinical information regarding ETD, which exhibits promising antimetastatic activity against non-small-cell lung cancer through Akt/mTOR/p70S6K-induced actin reorganization and MMPs expression.
Computational characterization of inhaled droplet transport to the nasopharynx
Authors: Basu Saikat 
Published: March 2021

AbstractHow human respiratory physiology and the transport phenomena associated with inhaled airflow in the upper airway proceed to impact transmission of SARS-CoV-2, leading to the initial infection, stays an open question. An answer can help determine the susceptibility of an individual on exposure to a COVID-2019 carrier and can also provide a preliminary projection of the still-unknown infectious dose for the disease. Computational fluid mechanics enabled tracking of respiratory transport in medical imaging-based anatomic domains shows that the regional deposition of virus-laden inhaled droplets at the initial nasopharyngeal infection site peaks for the droplet size range of approximately 2.5–19 $$\upmu $$
μ
. Through integrating the numerical findings on inhaled transmission with sputum assessment data from hospitalized COVID-19 patients and earlier measurements of ejecta size distribution generated during regular speech, this study further reveals that the number of virions that may go on to establish the SARS-CoV-2 infection in a subject could merely be in the order of hundreds.
Neural encoding of voice pitch and formant structure at birth as revealed by frequency-following responses
Authors: Arenillas-Alcón Sonia , Costa-Faidella Jordi , Ribas-Prats Teresa , Gómez-Roig María Dolores , Escera Carles 
Published: March 2021

AbstractDetailed neural encoding of voice pitch and formant structure plays a crucial role in speech perception, and is of key importance for an appropriate acquisition of the phonetic repertoire in infants since birth. However, the extent to what newborns are capable of extracting pitch and formant structure information from the temporal envelope and the temporal fine structure of speech sounds, respectively, remains unclear. Here, we recorded the frequency-following response (FFR) elicited by a novel two-vowel, rising-pitch-ending stimulus to simultaneously characterize voice pitch and formant structure encoding accuracy in a sample of neonates and adults. Data revealed that newborns tracked changes in voice pitch reliably and no differently than adults, but exhibited weaker signatures of formant structure encoding, particularly at higher formant frequency ranges. Thus, our results indicate a well-developed encoding of voice pitch at birth, while formant structure representation is maturing in a frequency-dependent manner. Furthermore, we demonstrate the feasibility to assess voice pitch and formant structure encoding within clinical evaluation times in a hospital setting, and suggest the possibility to use this novel stimulus as a tool for longitudinal developmental studies of the auditory system.
Selective time-dependent changes in activity and cell-specific gene expression in human postmortem brain
Authors: Dachet Fabien , Brown James B. , Valyi-Nagy Tibor , Narayan Kunwar D. , Serafini Anna , Boley Nathan , Gingeras Thomas R. , Celniker Susan E. , Mohapatra Gayatry , Loeb Jeffrey A. 
Published: March 2021

AbstractAs a means to understand human neuropsychiatric disorders from human brain samples, we compared the transcription patterns and histological features of postmortem brain to fresh human neocortex isolated immediately following surgical removal. Compared to a number of neuropsychiatric disease-associated postmortem transcriptomes, the fresh human brain transcriptome had an entirely unique transcriptional pattern. To understand this difference, we measured genome-wide transcription as a function of time after fresh tissue removal to mimic the postmortem interval. Within a few hours, a selective reduction in the number of neuronal activity-dependent transcripts occurred with relative preservation of housekeeping genes commonly used as a reference for RNA normalization. Gene clustering indicated a rapid reduction in neuronal gene expression with a reciprocal time-dependent increase in astroglial and microglial gene expression that continued to increase for at least 24 h after tissue resection. Predicted transcriptional changes were confirmed histologically on the same tissue demonstrating that while neurons were degenerating, glial cells underwent an outgrowth of their processes. The rapid loss of neuronal genes and reciprocal expression of glial genes highlights highly dynamic transcriptional and cellular changes that occur during the postmortem interval. Understanding these time-dependent changes in gene expression in post mortem brain samples is critical for the interpretation of research studies on human brain disorders.
Localized electronic vacancy level and its effect on the properties of doped manganites
Authors: Juan Dilson , Pruneda Miguel , Ferrari Valeria 
Published: March 2021

AbstractOxygen vacancies are common to most metal oxides and usually play a crucial role in determining the properties of the host material. In this work, we perform ab initio calculations to study the influence of vacancies in doped manganites $$\text {La}_{(1-\text {x})} \text {Sr}_{\text {x}} \text {MnO}_{3}$$

La

(
1
-
x
)

Sr
x

MnO
3

, varying both the vacancy concentration and the chemical composition within the ferromagnetic-metallic range ($$0.2\,<\,\text {x}\,<\,0.5$$

0.2

<

x

<

0.5

). We find that oxygen vacancies give rise to a localized electronic level and analyse the effects that the possible occupation of this defect state can have on the physical properties of the host. In particular, we observe a substantial reduction of the exchange energy that favors spin-flipped configurations (local antiferromagnetism), which correlate with the weakening of the double-exchange interaction, the deterioration of the metallicity, and the degradation of ferromagnetism in reduced samples. In agreement with previous studies, vacancies give rise to a lattice expansion when the defect level is unoccupied. However, our calculations suggest that under low Sr concentrations the defect level can be populated, which conversely results in a local reduction of the lattice parameter. Although the exact energy position of this defect level is sensitive to the details of the electronic interactions, we argue that it is not far from the Fermi energy for optimally doped manganites ($$\text {x}\,\sim \,1/3$$

x

∼

1
/
3

), and thus its occupation could be tuned by controlling the number of available electrons, either with chemical doping or gating. Our results could have important implications for engineering the electronic properties of thin films in oxide compounds.
A high-efficiency Klebsiella variicola H12-CMC-FeS@biochar for chromium removal from aqueous solution
Authors: Yu Runlan , Man Meilian , Yu Zhaojing , Wu Xueling , Shen Li , Liu Yuandong , Li Jiaokun , Xia Mingchen , Zeng Weimin 
Published: March 2021

AbstractIn polluted groundwater, surface water, and industrial sites, chromium is found as one of the most common heavy metals, and one of the 20 main pollutants in China, which poses a great threat to the ecological environment and human health. Combining biological and chemical materials to treat groundwater contaminated by heavy metals is a promising restoration technology. In this research, Klebsiella variicola H12 (abbreviated as K. variicola) was found to have Cr(VI) reduction ability. A high-efficiency Klebsiella variicola H12-carboxymethyl cellulose (abbreviated as CMC)-FeS@biochar system was established for Cr(VI) removal from aqueous solution. The Scanning Electron Microscope-Energy Dispersive Spectrometer (SEM–EDS), X-ray photoelectron spectroscopy (XPS) results indicated that CMC-FeS was successfully loaded onto the surface of biochar, and K. variicola H12 grew well in the presence of CMC-FeS@biochar with microbial biomass up to 4.8 × 108 cells mL−1. Cr(VI) removal rate of CMC-FeS@biochar system, K. variicola H12 system and K. variicola H12 + CMC-FeS@biochar system were 61.8%, 82.2% and 96.6% respectively. This study demonstrated K. variicola H12-CMC-FeS@biochar system have potential value for efficient removal of Cr(VI) from Cr(VI)-polluted groundwater.
Serum artemin is not correlated with sensitivity within dogs with naturally occurring osteoarthritis pain
Authors: Gupta Ankita , Chiavaccini Ludovica , Minnema Laura M. , Chiu King Wa , Knazovicky David , Hash Jonathan A. , Mishra Santosh K. , Lascelles B. Duncan X. 
Published: March 2021

AbstractOsteoarthritis (OA) pain is associated with peripheral and central sensitization in humans and results in widespread increased sensitivity across the body. Sensitization contributes to the OA-associated pain (OAP) state. We recently identified increased levels of an endogenous neurotrophic factor, artemin (ARTN), in dogs with OAP compared to healthy pain-free controls. Circulating ARTN released from damaged tissues in OA, may play a central role in widespread sensitivity and pain. However, the relationship between ARTN and somatosensory sensitivity remains unknown. The study aimed to assess the relationship between serum ARTN concentrations and measures of sensitivity in dogs with OAP using quantitative sensory testing. We hypothesized that there would be a positive association between circulating ARTN and increased sensitivity to mechanical and thermal stimuli in dogs with OAP. We used linear and logistic regression models to assess the relationship between ARTN, sensitization, and pain within a cohort of 43 dogs with spontaneous OAP. Serum ARTN was not associated with the degree of sensitization within dogs with OAP. Further, across dogs with varying OAP severity, we did not find any association between ARTN, and clinical measures of joint pain and disability. Although a relationship between ARTN and joint pain was not ruled out.