bluuebunny/crossref_metadata_2025_split huggingface dataset:
On Representative Elementary Volumes of Grayscale Micro‐CT Images of Porous Media
Authors: Singh Ankita , Regenauer‐Lieb Klaus , Walsh Stuart D. C. , Armstrong Ryan T. , van Griethuysen Joost J. M. , Mostaghimi Peyman 
Published: July 2020

AbstractThe concept of linking pore‐scale data to continuum‐scale characteristics of porous media relies on the existence of a representative elementary volume (REV). The current techniques for estimating REVs require access to segmented micro‐computed tomographic (micro‐CT) images and computations of petrophysical properties which are computationally intensive and time‐consuming. Herein, a texture characterization method called the Gray‐Level Size Zone Matrix (GLSZM) is applied directly to raw grayscale micro‐CT images. GLSZM representations of 3D micro‐CT images capture information regarding the connectivity of gray‐level intensities, termed as “size‐zones.” Statistical descriptors of pore space are calculated based on GLSZM to understand the connectivity of low gray‐level intensities. These GLSZM statistics capture microstructural fluctuations and offer insights into the impact of grayscale heterogeneity on REV size. This approach allows REV sizes to be estimated directly using grayscale micro‐CT images, in a reproducible, less time‐consuming and computationally efficient manner.
Direct Observation of Shock‐Induced Disordering of Enstatite Below the Melting Temperature
Authors: Hernandez J.‐A. , Morard G. , Guarguaglini M. , Alonso‐Mori R. , Benuzzi‐Mounaix A. , Bolis R. , Fiquet G. , Galtier E. , Gleason A. E. , Glenzer S. , Guyot F. , Ko B. , Lee H. J. , Mao W. L. , Nagler B. , Ozaki N. , Schuster A. K. , Shim S. H. , Vinci T. , Ravasio A. 
Published: July 2020

AbstractWe report in situ structural measurements of shock‐compressed single crystal orthoenstatite up to 337 ± 55 GPa on the Hugoniot, obtained by coupling ultrafast X‐ray diffraction to laser‐driven shock compression. Shock compression induces a disordering of the crystalline structure evidenced by the appearance of a diffuse X‐ray diffraction signal at nanosecond timescales at 80 ± 13 GPa on the Hugoniot, well below the equilibrium melting pressure (>170 GPa). The formation of bridgmanite and post‐perovskite have been indirectly reported in microsecond‐scale plate‐impact experiments. Therefore, we interpret the high‐pressure disordered state we observed at nanosecond scale as an intermediate structure from which bridgmanite and post‐perovskite crystallize at longer timescales. This evidence of a disordered structure of MgSiO3 on the Hugoniot indicates that the degree of polymerization of silicates is a key parameter to constrain the actual thermodynamics of shocks in natural environments.
A Dynamical Framework for Interpreting Ancient Sea Surface Temperatures
Authors: Judd Emily J. , Bhattacharya Tripti , Ivany Linda C. 
Published: July 2020

AbstractEfforts to estimate past global mean temperature and latitudinal gradients must contend with spatial heterogeneity in sea surface temperatures (SSTs). Here, we use modern SSTs to show that the environments from which most paleoclimatic data are drawn, shallow epeiric seas and continental margins, are systematically offset from zonal mean temperatures. Epeiric seas are warmer and more seasonal than open‐ocean values from the same latitudes, while continental margins exhibit consistent and predictable deviations related to gyre circulation. Warm temperatures inferred from Paleozoic proxy data may largely reflect that these data derive almost entirely from epeiric seas. Moreover, pseudoproxy analysis using Paleogene sampling localities demonstrates how undersampling of the full range of dynamical environments associated with gyre circulation can generate spurious estimates of latitudinal temperature gradients. Recognition of these global patterns permits a predictive framework within which to more robustly interpret proxy data, improve Earth system models, and reconstruct ancient dynamic regimes.
Record‐Low Arctic Stratospheric Ozone in 2020: MLS Observations of Chemical Processes and Comparisons With Previous Extreme Winters
Authors: Manney Gloria L. , Livesey Nathaniel J. , Santee Michelle L. , Froidevaux Lucien , Lambert Alyn , Lawrence Zachary D. , Millán Luis F. , Neu Jessica L. , Read William G. , Schwartz Michael J. , Fuller Ryan A. 
Published: July 2020

AbstractAura Microwave Limb Sounder (MLS) measurements show that chemical processing was critical to the observed record‐low Arctic stratospheric ozone in spring 2020. The 16‐year MLS record indicates more polar denitrification and dehydration in 2019/2020 than in any Arctic winter except 2015/2016. Chlorine activation and ozone depletion began earlier than in any previously observed winter, with evidence of chemical ozone loss starting in November. Active chlorine then persisted as late into spring as it did in 2011. Empirical estimates suggest maximum chemical ozone losses near 2.8 ppmv by late March in both 2011 and 2020. However, peak chlorine activation, and thus peak ozone loss, occurred at lower altitudes in 2020 than in 2011, leading to the lowest Arctic ozone values ever observed at potential temperature levels from ∼400–480 K, with similar ozone values to those in 2011 at higher levels.
East Asia Atmospheric River catalog: Annual Cycle, Transition Mechanism, and Precipitation
Authors: Pan Mengxin , Lu Mengqian 
Published: July 2020

AbstractAn all‐season East Asia Atmospheric River (EA AR) catalog is constructed based on PanLu2.0. The annual cycle of EA AR exhibits eight stages, synchronizing with the seasonal‐to‐subseasonal variation of precipitation and their associated atmospheric steering. Particularly, extension of the western North Pacific subtropical high (WNPSH) to south China sea, due to the springtime east‐west thermal contrast, steers ARs over Southeast China (SEC), inducing spring precipitation. During the Asian summer monsoon season, the spatial variation of the AR main route echoes the northward displacement of WNPSH, coincides with the prevailing monsoonal wind onset and stepwise propagation of rain belt. The warm moisture‐laden air of the wintertime ARs confronts the dry and cold air over SEC, contributing to the winter precipitation. ARs offer substantial potential predictability of (heavy) precipitation days over the midlatitude from the late spring to early summer, and over SEC and south Japan from late winter to early spring.
What Is a Debris Flood?
Authors: Church Michael , Jakob Matthias 
Published: July 2020

AbstractDebris floods have been defined descriptively as mineral and organic sediment‐rich floods, occurring in a steep channel and potentially destabilizing the streambed and banks. While this definition allows one to visualize the process, it does not inform on the mechanics, nor does it recognize different types. We propose to define debris floods as “floods during which the entire bed, possibly barring the very largest clasts, becomes mobile for at least a few minutes and over a length scale of at least 10 times the channel width.” We define the onset of a debris flood by the exceedance of a critical shear stress threshold required to mobilize at least the D84 of bed material. A threefold classification is proposed in which the first type is triggered by the shear stress exceedance. The second is initiated by transition from a debris flow either in the channel or by oblique impact of a debris‐flow‐prone tributary. In this context we highlight the importance of effective fluid density. The third type is associated with outbreak floods from artificial or natural dams. A further subdivision of debris floods is made by using the ratio of the actual shear stress to the critical shear stress, with higher values indicating damaging and finally catastrophic debris floods in which even preexisting channel bank and bed protection is mobilized. This contribution aims to provide a more succinct mechanistic definition of debris floods that can be implemented in hazard and risk assessments for steep streams and rivers.
The gut microbiota of brood parasite and host nestlings reared within the same environment: disentangling genetic and environmental effects
Authors: Lee Chop Yan , Peralta-Sánchez Juan Manuel , Martínez-Bueno Manuel , Møller Anders Pape , Rabelo-Ruiz Miguel , Zamora-Muñoz Carmen , Soler Juan José 
Published: July 2020

Abstract
Gut microbiota are essential for host health and survival, but we are still far from understanding the processes involved in shaping their composition and evolution. Controlled experimental work under lab conditions as well as human studies pointed at environmental factors (i.e., diet) as the main determinant of the microbiota with little evidence of genetic effects, while comparative interspecific studies detected significant phylogenetic effects. Different species, however, also differ in diet, feeding behavior, and environmental characteristics of habitats, all of which also vary interspecifically, and, therefore, can potentially explain most of the detected phylogenetic patterns. Here, we take advantage of the reproductive strategy of avian brood parasites and investigate gut microbiotas (esophageal (food and saliva) and intestinal) of great spotted cuckoo (Clamator glandarius) and magpie (Pica pica) nestlings that grow in the same nests. We also estimated diet received by each nestling and explored its association with gut microbiota characteristics. Although esophageal microbiota of magpies and great spotted cuckoos raised within the same environment (nest) did not vary, the microbiota of cloacal samples showed clear interspecific differences. Moreover, diet of great spotted cuckoo and magpie nestlings explained the microbiota composition of esophageal samples, but not of cloaca samples. These results strongly suggest a genetic component determining the intestinal microbiota of host and parasitic bird species, indicating that interspecific differences in gut morphology and physiology are responsible for such interspecific differences.
A combination of AZD5363 and FH5363 induces lethal autophagy in transformed hepatocytes
Authors: Patra Tapas , Meyer Keith , Ray Ratna B. , Ray Ranjit 
Published: July 2020

AbstractHepatocellular carcinoma (HCC) is one of the major causes of cancer-related death worldwide. High Akt activation and aberrant β-catenin expression contribute to HCC cell proliferation, stem cell generation, and metastasis. Several signaling pathway-specific inhibitors are in clinical trials and display different efficacies against HCC. In this study, we observed that a β-catenin inhibitor (FH535) displays antiproliferative effect on transformed human hepatocytes (THH). A combination treatment of these cells with FH535 and Akt inhibitor (AZD5363) exerted a stronger effect on cell death. Treatment of THH with AZD5363 and FH535 inhibited cell-cycle progression, enhanced autophagy marker protein expression, and autophagy-associated death, while FH535 treatment alone induced apoptosis. The use of chloroquine or z-VAD further verified these observations. Autophagy flux was evident from lowering marker proteins LAMP2, LAPTM4B, and autophagic protein expression by confocal microscopy using mCherry-EGFP-LC3 reporter construct. A combination treatment with AZD5363 and FH535 enhanced p53 expression, by modulating MDM2 activation; however, AZD5363 treatment alone restricted p53 to the nucleus by inhibiting dynamin-related protein activation. Nuclear p53 plays a crucial role for activation of autophagy by regulating the AMPK–mTOR-ULK1 pathway. Hep3B cells with null p53 did not modulate autophagy-dependent death from combination treatment. Together, our results strongly suggested that a combination treatment of Akt and β-catenin inhibitors exhibits efficient therapeutic potential for HCC.
Itraconazole inhibits the Hedgehog signaling pathway thereby inducing autophagy-mediated apoptosis of colon cancer cells
Authors: Deng Huiming , Huang Ling , Liao Zhongkai , Liu Mi , Li Qiang , Xu Ronghua 
Published: July 2020

AbstractItraconazole is as an antifungal medication used to treat systemic fungal infections. Recently, it has been reported to be effective in suppressing tumor growth by inhibiting the Hedgehog signaling pathway and angiogenesis. In the present study, we investigated whether itraconazole induces autophagy-mediated cell death of colon cancer cells through the Hedgehog signaling pathway. Cell apoptosis and cell cycle distribution of the colon cancer cell lines SW-480 and HCT-116 were detected by flow cytometry and terminal TUNEL assay. Autophagy and signal proteins were detected by western blotting and cell proliferation-associated antigen Ki-67 was measured using immunohistochemistry. The images of autophagy flux and formation of autophagosomes were observed by laser scanning confocal and/or transmission electron microscopy. Colon cancer cell xenograft mouse models were also established. Itraconazole treatment inhibited cell proliferation via G1 cell cycle arrest as well as autophagy-mediated apoptosis of SW-480 and HCT-116 colon cancer cells. In addition, the Hedgehog pathway was found to be involved in activation of itraconazole-mediated autophagy. After using the Hedgehog agonist recombinant human Sonic Hedgehog (rhshh), itraconazole could counteract the activation of rhshh. Moreover, treatment with itraconazole produced significant cancer inhibition in HCT-116-bearing mice. Thus, itraconazole may be a potential and effective therapy for the treatment of colon cancer.
A clinical study of patients with novel CDHR1 genotypes associated with late-onset macular dystrophy
Authors: Ba-Abbad Rola , Robson Anthony G. , Mahroo Omar A. , Wright Genevieve , Schiff Elena , Duignan Emma S. , Michaelides Michel , Arno Gavin , Webster Andrew R. 
Published: July 2020

Abstract
Purpose
To describe the clinical and electrophysiological features of adult-onset macular dystrophy, due to novel combinations of CDHR1 alleles, and compare the associated phenotypes with previous reports.

Methods
The clinical records of patients with macular dystrophy and biallelic variants in CDHR1 were reviewed. Data analysed included best corrected visual acuity (BCVA), fundus images: autofluorescence (AF) and optical coherence tomography (OCT); full field electroretinography (ERG) and pattern ERG (PERG).

Results
Seven patients from six pedigrees were ascertained. One patient was homozygous for a known synonymous variant p.(Pro261=), four were compound heterozygous for the p.(Pro261=) variant and a novel allele of CDHR1: p.(Gly188Ser), p.(Met1?), or p.(Val458Asp); one patient was compound heterozygous for two previously unreported variants: c.297+1G>T in trans with p.(Pro735Thr). The range of BCVA at the last clinic review was (6/5–6/60). Autofluorescence showed macular flecks of increased AF in mild cases and patches of reduced AF in severe cases. The OCT showed attenuation of the ellipsoid zone (EZ) in mild cases and loss of the EZ and the outer nuclear layer in severe cases; one patient had subfoveal hyporeflective region between the EZ and the retinal pigment epithelium. The full field ERG was normal or borderline subnormal in all cases, and the PERG was subnormal in mild cases or undetectable in severe cases.

Conclusions
This report corroborates previous observations that genotypes distinct from those causing pan-retinal dystrophy can cause a milder phenotype, predominantly affecting the macula, and expands the spectrum of these genotypes. The findings in this cohort suggest a potential macular susceptibility to mild perturbations of the photoreceptor cadherin.
BRCA1-associated structural variations are a consequence of polymerase theta-mediated end-joining
Authors: Kamp J. A. , van Schendel R. , Dilweg I. W. , Tijsterman M. 
Published: July 2020

AbstractFailure to preserve the integrity of the genome is a hallmark of cancer. Recent studies have revealed that loss of the capacity to repair DNA breaks via homologous recombination (HR) results in a mutational profile termed BRCAness. The enzymatic activity that repairs HR substrates in BRCA-deficient conditions to produce this profile is currently unknown. We here show that the mutational landscape of BRCA1 deficiency in C. elegans closely resembles that of BRCA1-deficient tumours. We identify polymerase theta-mediated end-joining (TMEJ) to be responsible: knocking out polq-1 suppresses the accumulation of deletions and tandem duplications in brc-1 and brd-1 animals. We find no additional back-up repair in HR and TMEJ compromised animals; non-homologous end-joining does not affect BRCAness. The notion that TMEJ acts as an alternative to HR, promoting the genome alteration of HR-deficient cells, supports the idea that polymerase theta is a promising therapeutic target for HR-deficient tumours.
Sensitivity and breadth of detection of high-throughput sequencing for adventitious virus detection
Authors: Charlebois Robert L. , Sathiamoorthy Sarmitha , Logvinoff Carine , Gisonni-Lex Lucy , Mallet Laurent , Ng Siemon H. S. 
Published: July 2020

AbstractHigh-throughput sequencing (HTS) is capable of broad virus detection encompassing both known and unknown adventitious viruses in a variety of sample matrices. We describe the development of a general-purpose HTS-based method for the detection of adventitious viruses. Performance was evaluated using 16 viruses equivalent to well-characterized National Institutes of Health (NIH) virus stocks and another six viruses of interest. A viral vaccine crude harvest and a cell substrate matrix were spiked with 22 viruses. Specificity was demonstrated for all 22 viruses at the species level. Our method was capable of detecting and identifying adventitious viruses spiked at 104 genome copies per milliliter in a viral vaccine crude harvest and 0.01 viral genome copies spiked per cell in a cell substrate matrix. Moreover, 9 of the 11 NIH model viruses with published in vivo data were detected by HTS with an equivalent or better sensitivity (in a viral vaccine crude harvest). Our general-purpose HTS method is unbiased and highly sensitive for the detection of adventitious viruses, and has a large breadth of detection, which may obviate the need to perform in vivo testing.
Entropy decay during grain growth
Authors: Vedanti Pawan , Wu Xin , Berdichevsky Victor 
Published: July 2020

AbstractMaterials with random microstructure are characterized by additional thermodynamic parameters, entropy and temperature of microstructure. It has been argued that there is one more law of thermodynamics: entropy of microstructure decays in isolated systems. In this paper, we check this assertion experimentally for the process of grain growth. We show that entropy of grain structure decays indeed as expected. We study also the equation of state for microstructure entropy. In general, microstructure entropy should be a function of microstructure energy and the average grain size. We observed that the equation of state degenerates, and there is a universal dependence of microstructure entropy on microstructure energy, at least at the stage of self similar grain growth.
Recurrence of positive SARS-CoV-2 viral RNA in recovered COVID-19 patients during medical isolation observation
Authors: Yuan Bo , Liu Han-Qing , Yang Zheng-Rong , Chen Yong-Xin , Liu Zhi-Yong , Zhang Kai , Wang Cheng , Li Wei-Xin , An Ya-Wen , Wang Jian-Chun , Song Shuo 
Published: July 2020

AbstractRecently, the recurrence of positive SARS-CoV-2 viral RNA in recovered COVID-19 patients is receiving more attention. Herein we report a cohort study on the follow-up of 182 recovered patients under medical isolation observation. Twenty (10.99%) patients out of the 182 were detected to be SARS-CoV-2 RNA positive (re-positives), although none showed any clinical symptomatic recurrence, indicating that COVID-19 responds well to treatment. Patients aged under 18 years had higher re-positive rates than average, and none of the severely ill patients re-tested positive. There were no significant differences in sex between re-positives and non-re-positives. Notably, most of the re-positives turned negative in the following tests, and all of them carried antibodies against SARS-CoV-2. This indicates that they might not be infectious, although it is still important to perform regular SARS-CoV-2 RNA testing and follow-up for assessment of infectivity. The findings of this study provide information for improving the management of recovered patients, and for differentiating the follow-up of recovered patients with different risk levels.
Hepcidin and ferritin levels in restless legs syndrome: a case–control study
Authors: Chenini Sofiene , Delaby Constance , Rassu Anna-Laura , Barateau Lucie , Vialaret Jérôme , Hirtz Christophe , Dupuy Anne Marie , Lehmann Sylvain , Jaussent Isabelle , Dauvilliers Yves 
Published: July 2020

AbstractThe association between restless legs syndrome (RLS) and iron homeostasis remains unclear. We compared serum hepcidin and ferritin levels in patients with RLS and controls, and assessed their relationships with RLS phenotype, drug intake, and history of augmentation syndrome. 102 drug-free RLS patients (age 58.9 [24.5–77.2], 63 females) and 73 controls (age 56.8 [23.46–76.6], 45 females) underwent a polysomnography recording. Hepcidin levels were quantified by ELISA. 34 RLS patients had a second assessment after starting dopaminergic drugs. Ferritin level was low (< 50 µg/l) in 14.7% of patients and 25% of controls, with no between-group differences in the mean values. Hepcidin levels were higher in patients even after adjustment for confounding factors, and excluding participants with low ferritin levels. Ferritin and hepcidin levels were comparable before and after treatment, and between patients with (n = 17) and without history of augmentation. Ferritin and hepcidin levels correlated with age, body mass index, and periodic leg movements. Higher hepcidin levels were associated with older age, older age at RLS onset, less daytime sleepiness and familial RLS. In conclusion, serum hepcidin levels but not ferritin were higher in RLS patients regardless of treatment and history of augmentation. Serum hepcidin may be a more relevant biomarker of RLS than ferritin.
Unraveling ecosystem functioning in intertidal soft sediments: the role of density-driven interactions
Authors: Schenone Stefano , Thrush Simon F. 
Published: July 2020

AbstractAlthough they only occupy a relatively small portion of the surface of the planet, coastal habitats are some of the most productive and valued ecosystems in the world. Among these habitats, tidal flats are an important component of many harbours and estuaries, but their deterioration due to human activities poses a serious threat to biodiversity and ecosystem function. Benthic communities are usually arranged in patches dominated by key species with overlapping distributions. Understanding the ecological consequences of interactions between these species in transition zones where their habitats overlap is necessary in order to quantify their contribution to overall ecosystem functioning and to scale-up and generalize results. Spatial transition in abundance and the interaction of multiple factors that drive ecosystem function are complex processes that require real-world research. Through a multi-site mensurative experiment, we show that transition areas drive non-linear effects on biogeochemical fluxes that have important implications for quantifying overall functioning. In our study the main drivers of ecosystem function were the abundance of two large but functionally very different species rather than biodiversity per se. Furthermore, we demonstrate that the use of the biogenic features created by specific infaunal species at the sediment–water interface is a better predictor of ecosystem functioning than the density of the species per se, making this approach particularly appealing for large scale, mapping and monitoring studies.