bluuebunny/crossref_metadata_2025_split huggingface dataset:
Can Lava Flow Like Water? Assessing Applications of Critical Flow Theory to Channelized Basaltic Lava Flows
Authors: Dietterich H. R. , Grant G. E. , Fasth B. , Major J. J. , Cashman K. V. 
Published: August 2022

AbstractFlowing lava and water have dramatically different physical properties but can form similar hydraulic structures, including undular hydraulic jumps, or standing wave trains. In water flows, undular hydraulic jumps are evidence of critical flow (Froude number ∼1) and open‐channel hydraulic theory provides a powerful tool for estimating flow depth and velocity. Monitoring these parameters in an active lava channel is inherently challenging, but essential for calculating lava discharge (effusion rate), a primary control on the rate of flow front advance and ultimate flow runout distance. We analyze undular hydraulic jumps in both water and lava flows to assess the conditions under which they form and, by extension, the potential use of critical flow theory to estimate, in real time, lava flow velocity, depth, and discharge. Experimental data for water flows show that these structures mark the transition from supercritical to subcritical flow. Undular hydraulic jumps in the near‐vent lava channel of the 2018 lower East Rift Zone eruption of Kīlauea, Hawaiʻi also reflect critical flow conditions; their wavelengths scale with flow depth and velocity, consistent with hydraulic theory. Calculated lava effusion rates are similar to estimates made using more traditional approaches (Jeffreys', 1925, https://doi.org/10.1080/14786442508634662, equation based on lava viscosity, density, and channel slope) and with lava volumes derived from topographic‐change mapping. From this we conclude that critical flow phenomena show great potential to track flow dynamics and inform hazard assessment for a wide range of geophysical fluids.
Chromatin conformation of human oral epithelium can identify orofacial cleft missing functional variants
Authors: Xiao Yao , Jiao Shengbo , He Miao , Lin Da , Zuo Huanyan , Han Jiahao , Sun Yonghua , Cao Gang , Chen Zhi , Liu Huan 
Published: August 2022

AbstractGenome-wide association studies (GWASs) are the most widely used method to identify genetic risk loci associated with orofacial clefts (OFC). However, despite the increasing size of cohort, GWASs are still insufficient to detect all the heritability, suggesting there are more associations under the current stringent statistical threshold. In this study, we obtained an integrated epigenomic dataset based on the chromatin conformation of a human oral epithelial cell line (HIOEC) using RNA-seq, ATAC-seq, H3K27ac ChIP-seq, and DLO Hi-C. Presumably, this epigenomic dataset could reveal the missing functional variants located in the oral epithelial cell active enhancers/promoters along with their risk target genes, despite relatively less-stringent statistical association with OFC. Taken a non-syndromic cleft palate only (NSCPO) GWAS data of the Chinese Han population as an example, 3664 SNPs that cannot reach the strict significance threshold were subjected to this functional identification pipeline. In total, 254 potential risk SNPs residing in active cis-regulatory elements interacting with 1 718 promoters of oral epithelium-expressed genes were screened. Gapped k-mer machine learning based on enhancers interacting with epithelium-expressed genes along with in vivo and in vitro reporter assays were employed as functional validation. Among all the potential SNPs, we chose and confirmed that the risk alleles of rs560789 and rs174570 reduced the epithelial-specific enhancer activity by preventing the binding of transcription factors related to epithelial development. In summary, we established chromatin conformation datasets of human oral epithelial cells and provided a framework for testing and understanding how regulatory variants impart risk for clefts.
Hepatic ARID3A facilitates liver cancer malignancy by cooperating with CEP131 to regulate an embryonic stem cell-like gene signature
Authors: Shen Mengting , Li Shengli , Zhao Yiming , Liu Yizhe , Liu Zhen , Huan Lin , Qiao Yejun , Wang Lu , Han Leng , Chen Zhiao , He Xianghuo 
Published: August 2022

AbstractLiver cancer stemness refers to the stem cell-like phenotype of hepatocarcinoma cells and is closely related to a high degree of tumour malignancy. Here, we identified AT-rich interacting domain 3A (ARID3A) as one of the most upregulated stemness-related transcription factors in liver cancer by an in vitro functional screen. ARID3A can promote liver cancer cell viability and metastasis both in vitro and in vivo. Mechanistically, ARID3A interacts with CEP131 and transcriptionally activates KDM3A by co-occupying its promoter element, further upregulating the expression of downstream embryonic stem (ES) signature genes via demethylation of H3K9me2. ARID3A and CEP131 promote an ES cell gene signature through activation of KDM3A and contribute to the poor prognosis of liver cancer patients. Collectively, these results provide evidence highlighting a transcription-dependent mechanism of ARID3A in stemness regulation in liver cancer. The ARID3A/CEP131-KDM3A regulatory circuit could serve as a prognostic indicator and potential therapeutic target for liver cancer.
Social inequalities in climate change-attributed impacts of Hurricane Harvey
Authors: Smiley Kevin T. , Noy Ilan , Wehner Michael F. , Frame Dave , Sampson Christopher C. , Wing Oliver E. J. 
Published: August 2022

AbstractClimate change is already increasing the severity of extreme weather events such as with rainfall during hurricanes. But little research to date investigates if, and to what extent, there are social inequalities in climate change-attributed extreme weather event impacts. Here, we use climate change attribution science paired with hydrological flood models to estimate climate change-attributed flood depths and damages during Hurricane Harvey in Harris County, Texas. Using detailed land-parcel and census tract socio-economic data, we then describe the socio-spatial characteristics associated with these climate change-induced impacts. We show that 30 to 50% of the flooded properties would not have flooded without climate change. Climate change-attributed impacts were particularly felt in Latina/x/o neighborhoods, and especially so in Latina/x/o neighborhoods that were low-income and among those located outside of FEMA’s 100-year floodplain. Our focus is thus on climate justice challenges that not only concern future climate change-induced risks, but are already affecting vulnerable populations disproportionately now.
Ultrafast pseudospin quantum beats in multilayer WSe2 and MoSe2
Authors: Raiber Simon , Faria Junior Paulo E. , Falter Dennis , Feldl Simon , Marzena Petter , Watanabe Kenji , Taniguchi Takashi , Fabian Jaroslav , Schüller Christian 
Published: August 2022

AbstractLayered van-der-Waals materials with hexagonal symmetry offer an extra degree of freedom to their electrons, the so-called valley index or valley pseudospin, which behaves conceptually like the electron spin. Here, we present investigations of excitonic transitions in mono- and multilayer WSe2 and MoSe2 materials by time-resolved Faraday ellipticity (TRFE) with in-plane magnetic fields, B∥, of up to 9 T. In monolayer samples, the measured TRFE time traces are almost independent of B∥, which confirms a close to zero in-plane exciton g factor g∥, consistent with first-principles calculations. In contrast, we observe pronounced temporal oscillations in multilayer samples for B∥ > 0. Our first-principles calculations confirm the presence of a non-zero g∥ for the multilayer samples. We propose that the oscillatory TRFE signal in the multilayer samples is caused by pseudospin quantum beats of excitons, which is a manifestation of spin- and pseudospin layer locking in the multilayer samples.
A polymer electrolyte design enables ultralow-work-function electrode for high-performance optoelectronics
Authors: Tong Bo , Du Jinhong , Yin Lichang , Zhang Dingdong , Zhang Weimin , Liu Yu , Wei Yuning , Liu Chi , Liang Yan , Sun Dong-Ming , Ma Lai-Peng , Cheng Hui-Ming , Ren Wencai 
Published: August 2022

AbstractAmbient solution-processed conductive materials with a sufficient low work function are essential to facilitate electron injection in electronic and optoelectronic devices but are challenging. Here, we design an electrically conducting and ambient-stable polymer electrolyte with an ultralow work function down to 2.2 eV, which arises from heavy n-doping of dissolved salts to polymer matrix. Such materials can be solution processed into uniform and smooth films on various conductors including graphene, conductive metal oxides, conducting polymers and metals to substantially improve their electron injection, enabling high-performance blue light-emitting diodes and transparent light-emitting diodes. This work provides a universal strategy to design a wide range of stable charge injection materials with tunable work function. As an example, we also synthesize a high-work-function polymer electrolyte material for high-performance solar cells.
Control cell migration by engineering integrin ligand assembly
Authors: Hu Xunwu , Roy Sona Rani , Jin Chengzhi , Li Guanying , Zhang Qizheng , Asano Natsuko , Asahina Shunsuke , Kajiwara Tomoko , Takahara Atsushi , Feng Bolu , Aoki Kazuhiro , Xu Chenjie , Zhang Ye 
Published: August 2022

AbstractAdvances in mechanistic understanding of integrin-mediated adhesion highlight the importance of precise control of ligand presentation in directing cell migration. Top-down nanopatterning limited the spatial presentation to sub-micron placing restrictions on both fundamental study and biomedical applications. To break the constraint, here we propose a bottom-up nanofabrication strategy to enhance the spatial resolution to the molecular level using simple formulation that is applicable as treatment agent. Via self-assembly and co-assembly, precise control of ligand presentation is succeeded by varying the proportions of assembling ligand and nonfunctional peptide. Assembled nanofilaments fulfill multi-functions exerting enhancement to suppression effect on cell migration with tunable amplitudes. Self-assembled nanofilaments possessing by far the highest ligand density prevent integrin/actin disassembly at cell rear, which expands the perspective of ligand-density-dependent-modulation, revealing valuable inputs to therapeutic innovations in tumor metastasis.
Advanced wastewater treatment and membrane fouling control by electro-encapsulated self-forming dynamic membrane bioreactor
Authors: Millanar-Marfa Jessa Marie J. , Corpuz Mary Vermi Aizza , Borea Laura , Cabreros Carlo , G. De Luna Mark Daniel , Ballesteros Florencio , Vigliotta Giovanni , Zarra Tiziano , Hasan Shadi W. , Korshin Gregory V. , Buonerba Antonio , Belgiorno Vincenzo , Naddeo Vincenzo 
Published: August 2022

AbstractAn advanced concept of aerobic membrane bioreactors (MBRs) for highly efficient wastewater treatment has been disclosed by introduction of an electro and encapsulated self-forming dynamic biomembrane (e-ESFDM). The biological filtering membrane is intercalated between two woven polyester fabrics as supports that assist the formation and protect the biomembrane. The innovative architecture of the e-ESFDM in combination with electrocoagulation processes resulted in efficient and cost-effective wastewater treatment and control of the membrane fouling. The performance of the e-ESFDMBR was compared to a yet highly efficient ESFDMBR, where the electric field was not present. The ESFDM-based reactors both showed comparable results in the removal of organic matter, in terms of COD and DOC. On the other hand, e-ESFDMBR exceeded the performance of the ESFDMBR in the reduction of nitrogen- and phosphorous-containing pollutants, responsible for eutrophication processes in the environment, and recalcitrant molecules, such as humic-like substances. In addition, an extremely low fouling rate was observed for the e-ESFDM bioreactor. Insights on the biological processes involved in the developed MBR were provided by investigations on the microbiological diversity found in reactor mixed liquor, ESFDM layer and treated wastewater.
Giant voltage amplification from electrostatically induced incipient ferroelectric states
Authors: Graf Mónica , Aramberri Hugo , Zubko Pavlo , Íñiguez Jorge 
Published: August 2022

AbstractFerroelectrics subject to suitable electric boundary conditions present a steady negative capacitance response1,2. When the ferroelectric is in a heterostructure, this behaviour yields a voltage amplification in the other elements, which experience a potential difference larger than the one applied, holding promise for low-power electronics3. So far research has focused on verifying this effect and little is known about how to optimize it. Here, we describe an electrostatic theory of ferroelectric/dielectric superlattices, convenient model systems4,5, and show the relationship between the negative permittivity of the ferroelectric layers and the voltage amplification in the dielectric ones. Then, we run simulations of PbTiO3/SrTiO3 superlattices to reveal the factors most strongly affecting the amplification. In particular, we find that giant effects (up to tenfold increases) can be obtained when PbTiO3 is brought close to the so-called ‘incipient ferroelectric’ state.
The NIMH intramural healthy volunteer dataset: A comprehensive MEG, MRI, and behavioral resource
Authors: Nugent Allison C. , Thomas Adam G. , Mahoney Margaret , Gibbons Alison , Smith Jarrod T. , Charles Antoinette J. , Shaw Jacob S. , Stout Jeffrey D. , Namyst Anna M. , Basavaraj Arshitha , Earl Eric , Riddle Travis , Snow Joseph , Japee Shruti , Pavletic Adriana J. , Sinclair Stephen , Roopchansingh Vinai , Bandettini Peter A. , Chung Joyce 
Published: August 2022

AbstractThe NIMH Healthy Research Volunteer Dataset is a collection of phenotypic data characterizing healthy research volunteers using clinical assessments such as assays of blood and urine, mental health assessments, diagnostic and dimensional measures of mental health, cognitive and neuropsychological functioning, structural and functional magnetic resonance imaging (MRI), along with diffusion tensor imaging (DTI), and a comprehensive magnetoencephalography battery (MEG). In addition, blood samples of healthy volunteers are banked for future analyses. All data collected in this protocol are broadly shared in the OpenNeuro repository, in the Brain Imaging Data Structure (BIDS) format. In addition, task paradigms and basic pre-processing scripts are shared on GitHub. There are currently few open access MEG datasets, and multimodal neuroimaging datasets are even more rare. Due to its depth of characterization of a healthy population in terms of brain health, this dataset may contribute to a wide array of secondary investigations of non-clinical and clinical research questions.
Understanding the genetics of viral drug resistance by integrating clinical data and mining of the scientific literature
Authors: Goto An , Rodriguez-Esteban Raul , Scharf Sebastian H. , Morris Garrett M. 
Published: August 2022

AbstractDrug resistance caused by mutations is a public health threat for existing and emerging viral diseases. A wealth of evidence about these mutations and their clinically associated phenotypes is scattered across the literature, but a comprehensive perspective is usually lacking. This work aimed to produce a clinically relevant view for the case of Hepatitis B virus (HBV) mutations by combining a chronic HBV clinical study with a compendium of genetic mutations systematically gathered from the scientific literature. We enriched clinical mutation data by systematically mining 2,472,725 scientific articles from PubMed Central in order to gather information about the HBV mutational landscape. By performing this analysis, we were able to identify mutational hotspots for each HBV genotype (A-E) and gene (C, X, P, S), as well as the location of disulfide bonds associated with these mutations. Through a modelling study, we also identified a mutation position common in both the clinical data and the literature that is located at the binding pocket for a known anti-HBV drug, namely entecavir. The results of this novel approach show the potential of integrated analyses to assist in the development of new drugs for viral diseases that are more robust to resistance. Such analyses should be of particular interest due to the increasing importance of viral resistance in established and emerging viruses, such as for newly developed drugs against SARS-CoV-2.
Atypical behavioral and thermoregulatory circadian rhythms in mice lacking a microbiome
Authors: Leone Vanessa A. , Onishi Kenneth G. , Kennedy Megan , Riggle Jonathan P. , Pierre Joseph F. , Maneval Andrew C. , Spedale Melanie N. , Theriault Betty R. , Chang Eugene B. , Prendergast Brian J. 
Published: August 2022

AbstractTrillions of microbial oscillators reside throughout the mammalian body, yet their contributions toward fundamental features of host circadian rhythms (CRs) have not been characterized. Here, we demonstrate that the microbiome contributes to host CRs in activity and thermoregulation. Mice devoid of microbes (germ-free, GF) exhibited higher-amplitude CRs in a light–dark cycle and longer circadian periods in constant darkness. Circadian entrainment to food was greater in GF mice, but resetting responses to simulated jet-lag were unaffected. Microbial transplantation with cecal contents of conventionally-raised mice normalized CRs of GF mice, indicating that the concurrent activity of gut microbes modulates host circadian networks. Obesogenic effects of high-fat diet were absent in GF mice, but some circadian-disruptive effects persisted. Transkingdom (host-microbe) interactions affect circadian period and entrainment of CRs in diverse traits, and microbes alter interactions among light- and food-entrainable circadian processes in the face of environmental (light, diet) perturbations.
New data from the first discovered paleoparadoxiid (Desmostylia) specimen shed light into the morphological variation of the genus Neoparadoxia
Authors: Matsui Kumiko , Valenzuela-Toro Ana M. , Pyenson Nicholas D. 
Published: August 2022

AbstractDesmostylia is an extinct clade of marine mammals with two major sub-clades, Desmostylidae and Paleoparadoxiidae, known from Oligocene to Miocene strata of the North Pacific coastline. Within Paleoparadoxiidae, three genera have been identified: Archaeoparadoxia, Paleoparadoxia, and Neoparadoxia. The latter taxon is the geochronologically youngest palaeoparadoxiid and Neoparadoxia is characterized by a comparatively larger body size, although it is known only from a few specimens within a short temporal and geographic range. Here we report the discovery of an isolated tooth, which we identify as Neoparadoxia cf. N. cecilialina, constituting only the second individual specimen of Neoparadoxia with preserved dentition yet reported. This specimen was collected near Corona, California, USA, and we attribute it to the “Topanga” Formation, extending the geographic range of this taxon in Southern California. While the exact geographic locality was not recorded when it was collected in 1913, we establish two potential localities based on associated hand-written museum label and new stratigraphic information. Although initially identified as Desmostylus hesperus, this specimen of Neoparadoxia was collected 10 years before the first named paleoparadoxiid from Japan. We expect that description of more complete desmostylian material from elsewhere in Southern California will clarify the taxonomic richness and paleoecological role of this clade in Cenozoic marine mammal assemblages.
Metformin administration is associated with enhanced response to transarterial chemoembolization for hepatocellular carcinoma in type 2 diabetes patients
Authors: Jung Woo Jin , Jang Sangmi , Choi Won Joon , Park Jaewon , Choi Gwang Hyeon , Jang Eun Sun , Jeong Sook-Hyang , Choi Won Seok , Lee Jae Hwan , Yoon Chang Jin , Kim Jin-Wook 
Published: August 2022

AbstractTransarterial chemoembolization (TACE) is often used as a locoregional therapy for early hepatocellular carcinoma (HCC) when local ablation or resection are not feasible, but incomplete response and recurrence are commonly observed. In this study, we sought to determine the association between metformin administration and TACE outcomes for single nodular HCC in patients with type 2 diabetes mellitus (T2DM). The retrospective cohort analysis included 164 T2DM patients with single nodular HCC who underwent TACE as an initial treatment, and 91 were exposed to metformin before and after TACE. Propensity score (PS) matching was used to balance covariates. Logistic regression analysis was used to determine the predictors of tumor response after TACE, and Cox regression analysis assessed independent predictors of local tumor recurrence (LTR) in patients with complete response after TACE. Metformin use was associated with significantly higher objective response rate (ORR) in the overall and PS-matched cohort (79.1% vs. 60.3 and 78.7% vs. 57.5%; p = 0.008 and p = 0.029, respectively). Logistic regression analysis showed that metformin use was an independent predictor of ORR in all and PS-matched patients (odds ratio = 2.65 and 3.06; p = 0.016 and 0.034, respectively). Cox regression analysis showed metformin administration was an independent predictor for lower LTR in all and PS-matched patients (hazard ratio = 0.28 and 0.27; p = 0.001 and 0.007, respectively). Metformin administration is associated with better initial response and lower local recurrence after TACE for single nodular HCC in T2DM.
Structural bioinformatics analysis of SARS-CoV-2 variants reveals higher hACE2 receptor binding affinity for Omicron B.1.1.529 spike RBD compared to wild type reference
Authors: Durmaz Vedat , Köchl Katharina , Krassnigg Andreas , Parigger Lena , Hetmann Michael , Singh Amit , Nutz Daniel , Korsunsky Alexander , Kahler Ursula , König Centina , Chang Lee , Krebs Marius , Bassetto Riccardo , Pavkov-Keller Tea , Resch Verena , Gruber Karl , Steinkellner Georg , Gruber Christian C. 
Published: August 2022

AbstractTo date, more than 263 million people have been infected with SARS-CoV-2 during the COVID-19 pandemic. In many countries, the global spread occurred in multiple pandemic waves characterized by the emergence of new SARS-CoV-2 variants. Here we report a sequence and structural-bioinformatics analysis to estimate the effects of amino acid substitutions on the affinity of the SARS-CoV-2 spike receptor binding domain (RBD) to the human receptor hACE2. This is done through qualitative electrostatics and hydrophobicity analysis as well as molecular dynamics simulations used to develop a high-precision empirical scoring function (ESF) closely related to the linear interaction energy method and calibrated on a large set of experimental binding energies. For the latest variant of concern (VOC), B.1.1.529 Omicron, our Halo difference point cloud studies reveal the largest impact on the RBD binding interface compared to all other VOC. Moreover, according to our ESF model, Omicron achieves a much higher ACE2 binding affinity than the wild type and, in particular, the highest among all VOCs except Alpha and thus requires special attention and monitoring.