bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Assessment of Organic Matter Young's Modulus Distribution With Depositional Environment and Maturity
Authors: Fender T. D. , Van Der Land C. , Rouainia M. , Graham S. P. , Jones D. M. , Vane C. H. , Wagner T. 
Published: October 2020

AbstractQuantification of risk to seal integrity in CCS, or gas extraction from hydraulic fracturing, is directly affected by the accessibility of organic pores within organic rich mudrocks. Knowledge of the host organic matter's mechanical properties, which are influenced by depositional environment and thermal maturity, are required to reduce operational risk. In this study we address the effect of both depositional environment and maturity on organic matter Young's modulus by means of Atomic Force Microscopy Quantitative ImagingTM, which is a nondestructive technique capable of nanomechanical measurements. Shales from varying marine depositional environments covering kerogen Types II (Barnett), IIS (Tarfaya), and II/III (Eagle Ford/ Bowland) are analyzed to capture variance in organic matter. The findings show organic matter has a Young's modulus ranging between 0.1 and 24 GPa. These marine shales have a bimodal distribution of Young's modulus to some degree, with peaks at between 3–10 and 19–24 GPa. These shales exhibit a trend with maturity, whereby Young's modulus values of <10 GPa are dominant in immature Tarfaya shale, becoming similar to the proportion of values above 15 GPa within the oil window, before the stiffer values dominate into the gas window. These peaks most likely represent soft heterogeneous aliphatic rich kerogen and stiff ordered aromatic rich kerogen, evidenced by the increase in the stiffer component with maturity and correlated with 13C NMR spectrocopy. These findings enable increased realism in microscale geomechanical fracture tip propagation models and may allow direct comparison between Young's modulus and Rock‐Eval parameters.
Interactions Between Mesoscale Eddies and Synoptic Oscillations in the Bay of Bengal During the Strong Monsoon of 2019
Authors: Greaser Samantha R. , Subrahmanyam Bulusu , Trott Corinne B. , Roman‐Stork Heather L. 
Published: October 2020

AbstractThe 2019 southwest monsoon season is the first strong monsoon in the last 25 years and occurred concurrently with a strong positive Indian Ocean Dipole (pIOD). Given these unique circumstances, we examine the mesoscale eddy field in the Bay of Bengal (BoB) during 2019 and the interactions between these eddies and 3–7‐day synoptic oscillations and tropical systems, which contribute to monsoon rainfall and modulate the active (wet) and break (dry) phases of the Indian monsoon. We find that there is a drastic difference in eddy characteristics between the western (80–90°E) and eastern (90–100°E) BoB, where eddies in the eastern BoB are dominated by coastal Kelvin wave (CKW) dynamics and topographical influences, and the eddies in the western BoB are more heavily modulated by East India Coastal Current dynamics. We further find that the pIOD increased the overall sea level in the BoB and modified CKW propagation in the BoB such that all eddy types had more positive sea level anomalies. We find that cyclonic eddies vary coherently with both upper ocean heat content and 3–7‐day bandpass filtered precipitation and that both the number of cyclonic eddies and eddy amplitude increase in coherence with precipitation and ocean heat content following the passage of a tropical system. These results suggest a strong relationship between cyclonic eddies and 3–7‐day atmospheric variability.
Soil Respiration Response to Rainfall Modulated by Plant Phenology in a Montane Meadow, East River, Colorado, USA
Authors: Winnick Matthew J. , Lawrence Corey R. , McCormick Maeve , Druhan Jennifer L. , Maher Kate 
Published: October 2020

AbstractSoil respiration is a primary component of the terrestrial carbon cycle. However, predicting the response of soil respiration to climate change remains a challenge due to the complex interactions between environmental drivers, especially plant phenology, temperature, and soil moisture. In this study, we use a 1‐D diffusion‐reaction model to calculate depth‐resolved CO2 production rates from soil CO2 concentrations and surface efflux observations in a subalpine meadow in the East River watershed, CO. Modeled rates are compared to in situ soil temperature and moisture conditions and MODIS satellite enhanced vegetation index (EVI) representing plant phenology across three hydrologically distinct growing seasons from 2016–2018. While soil respiration correlated with temperature on diel timescales (p < 0.05), seasonal variability was dominated by soil moisture and plant phenology (p < 0.05). We observed significant respiration increases in response to precipitation events; however, magnitude and duration were significantly higher in 2017 than 2016 despite similar wetting characteristics. Based on MODIS EVI, we suggest that the respiration response to rainfall is controlled by plant phenology, which in turn reflects the capacity of plants to respond to precipitation via increased photosynthesis and autotrophic respiration, behavior that is not captured in typical soil respiration pulse models. Projected changes in montane climate such as earlier snowmelt and prolonged fore‐summer drought may decrease soil respiration fluxes by decreasing the overlap between peak productivity and the summer monsoon. Finally, we observed significant late season CO2 fluxes from the deep subsoil (>165 cm) that support growing evidence for the importance of subsoil processes in driving integrated respiration fluxes.
Impact of novel coronavirus disease (COVID-19) on Egyptian dentists’ fear and dental practice (a cross-sectional survey)
Authors: Aly Mariam Mohsen , Elchaghaby Marwa Aly 
Published: October 2020

Abstract
Objectives
This study aimed to evaluate the fear of infection among Egyptian dentists practicing during the current coronavirus disease 2019 (COVID-19) pandemic and to explore the dentist’s knowledge about guidelines to fight the virus and to assess various modifications in dental practice.

Methods
An online survey was submitted to dental professionals. Data were collected through a validated questionnaire consisting of 23 closed-ended questions. The gathered data were statistically analyzed.

Results
An overall 216 dentists completed the survey. A total of 200 (92.6%) dental professionals were afraid of becoming infected with COVID-19 while 196 (90.7%) became anxious to treat patients showing suspicious symptoms. The majority of the participants were aware of the mode of transmission of COVID-19 and a lot of them were updated with the current Disease Control and Prevention (CDC) or World Health Organization (WHO) guidelines for cross-infection control.

Conclusions
COVID-19 pandemic has a significant impact on dental professionals.
Splicing factor SF3B1 promotes endometrial cancer progression via regulating KSR2 RNA maturation
Authors: Popli Pooja , Richters Megan M. , Chadchan Sangappa B. , Kim Tae Hoon , Tycksen Eric , Griffith Obi , Thaker Premal H. , Griffith Malachi , Kommagani Ramakrishna 
Published: October 2020

AbstractAlthough endometrial cancer is the most common cancer of the female reproductive tract, we have little understanding of what controls endometrial cancer beyond the transcriptional effects of steroid hormones such as estrogen. As a result, we have limited therapeutic options for the ~62,000 women diagnosed with endometrial cancer each year in the United States. Here, in an attempt to identify new prognostic and therapeutic targets, we focused on a new area for this cancer—alternative mRNA splicing—and investigated whether splicing factor, SF3B1, plays an important role in endometrial cancer pathogenesis. Using a tissue microarray, we found that human endometrial tumors expressed more SF3B1 protein than non-cancerous tissues. Furthermore, SF3B1 knockdown reduced in vitro proliferation, migration, and invasion of the endometrial cancer cell lines Ishikawa and AN3CA. Similarly, the SF3B1 inhibitor, Pladienolide-B (PLAD-B), reduced the Ishikawa and AN3CA cell proliferation and invasion in vitro. Moreover, PLAD-B reduced tumor growth in an orthotopic endometrial cancer mouse model. Using RNA-Seq approach, we identified ~2000 differentially expressed genes (DEGs) with SF3B1 knockdown in endometrial cancer cells. Additionally, alternative splicing (AS) events analysis revealed that SF3B1 depletion led to alteration in multiple categories of AS events including alternative exon skipping (ES), transcript start site usage (TSS), and transcript termination site (TTS) usage. Subsequently, bioinformatics analysis showed KSR2 as a potential candidate for SF3B1-mediated functions in endometrial cancer. Specifically, loss of SF3B1 led to decrease in KSR2 expression, owing to reduced maturation of KSR2 pre-mRNA to a mature RNA. Importantly, we found rescuing the KSR2 expression with SF3B1 knockdown partially restored the cell growth of endometrial cancer cells. Taken together, our data suggest that SF3B1 plays a crucial oncogenic role in the tumorigenesis of endometrial cancer and hence may support the development of SF3B1 inhibitors to treat this disease.
USP7 mediates pathological hepatic de novo lipogenesis through promoting stabilization and transcription of ZNF638
Authors: Ni Wenkai , Lin Shengli , Bian Saiyan , Zheng Wenjie , Qu Lishuai , Fan Yihui , Lu Cuihua , Xiao Mingbing , Zhou Pinghong 
Published: October 2020

AbstractAberrant de novo lipogenesis (DNL) results in excessive hepatic lipid accumulation and liver steatosis, the causative factors of many liver diseases, such as non-alcoholic fatty liver disease (NAFLD), non-alcoholic steatohepatitis (NASH), and hepatocellular carcinoma (HCC). However, the underlying mechanism of DNL dysregulation remains largely unknown. Ubiquitination of proteins in hepatocytes has been shown to be widely involved in lipid metabolism of liver. Here, we revealed that Ubiquitin-specific peptidase 7 (USP7), a deubiquitinase (DUB), played key roles in DNL through regulation of zinc finger protein 638 (ZNF638) in hepatocytes. USP7 has been shown not only to interact with and deubiquitylate ZNF638, but also to facilitate the transcription of ZNF638 via the stabilization of cAMP responsive element binding protein (CREB). USP7/ZNF638 axis selectively increased the cleavage of sterol regulatory element binding protein (SREBP1C) through AKT/mTORC1/S6K signaling, and formed USP7/ZNF638/SREBP1C nuclear complex to regulate lipogenesis-associated enzymes, including acetyl-CoA carboxylase (ACACA), fatty acid synthase (FASN), and Stearoyl-CoA desaturase (SCD). In the mice liver steatosis model induced by fructose, USP7 or ZNF638 abrogation significantly ameliorated disease progression. Furthermore, USP7/ZNF638 axis participated in the progression of lipogenesis-associated HCC. Our results have uncovered a novel mechanism of hepatic DNL, which might be beneficial to the development of new therapeutic targets for hepatic lipogenesis-associated diseases.
Long noncoding RNA FGF14-AS2 inhibits breast cancer metastasis by regulating the miR-370-3p/FGF14 axis
Authors: Jin Yucui , Zhang Ming , Duan Rui , Yang Jiashu , Yang Ying , Wang Jue , Jiang Chaojun , Yao Bing , Li Lingyun , Yuan Hongyan , Zha Xiaoming , Ma Changyan 
Published: October 2020

AbstractLong noncoding RNAs (lncRNAs) have emerged as important regulators in cancers, including breast cancer. However, the overall biological roles and clinical significance of most lncRNAs are not fully understood. This study aimed to elucidate the potential role of a novel lncRNA FGF14-AS2 and the mechanisms underlying metastasis in breast cancer. The lncRNA FGF14-AS2 was significantly downregulated in breast cancer tissues; patients with lower FGF14-AS2 expression had advanced clinical stage. In vitro and in vivo assays of FGF14-AS2 alterations revealed a complex integrated phenotype affecting breast cancer cell migration, invasion, and tumor metastasis. Mechanistically, FGF14-AS2 functioned as a competing endogenous RNA of miR-370-3p, thereby leading to the activation of its coding counterpart, FGF14. Clinically, we observed increased miR-370-3p expression in breast cancer tissues, whereas FGF14 expression was decreased in breast cancer tissues compared to the adjacent normal breast tissues. FGF14-AS2 expression was significantly negatively correlated with miR-370-3p expression, and correlated positively to FGF14 expression. Collectively, our findings support a model in which the FGF14-AS2/miR-370-3p/FGF14 axis is a critical regulator in breast cancer metastasis, suggesting a new therapeutic direction in breast cancer.
Autism spectrum disorder-like behavior caused by reduced excitatory synaptic transmission in pyramidal neurons of mouse prefrontal cortex
Authors: Sacai Hiroaki , Sakoori Kazuto , Konno Kohtarou , Nagahama Kenichiro , Suzuki Honoka , Watanabe Takaki , Watanabe Masahiko , Uesaka Naofumi , Kano Masanobu 
Published: October 2020

AbstractAutism spectrum disorder (ASD) is thought to result from deviation from normal development of neural circuits and synaptic function. Many genes with mutation in ASD patients have been identified. Here we report that two molecules associated with ASD susceptibility, contactin associated protein-like 2 (CNTNAP2) and Abelson helper integration site-1 (AHI1), are required for synaptic function and ASD-related behavior in mice. Knockdown of CNTNAP2 or AHI1 in layer 2/3 pyramidal neurons of the developing mouse prefrontal cortex (PFC) reduced excitatory synaptic transmission, impaired social interaction and induced mild vocalization abnormality. Although the causes of reduced excitatory transmission were different, pharmacological enhancement of AMPA receptor function effectively restored impaired social behavior in both CNTNAP2- and AHI1-knockdown mice. We conclude that reduced excitatory synaptic transmission in layer 2/3 pyramidal neurons of the PFC leads to impaired social interaction and mild vocalization abnormality in mice.
Interglacials of the Quaternary defined by northern hemispheric land ice distribution outside of Greenland
Authors: Köhler Peter , van de Wal Roderik S. W. 
Published: October 2020

AbstractGlacial/interglacial dynamics during the Quaternary were suggested to be mainly driven by obliquity (41-kyr periodicity), including irregularities during the last 1 Myr that resulted in on average 100-kyr cycles. Here, we investigate this so-called Mid-Pleistocene Transition via model-based deconvolution of benthic δ18O, redefining interglacials by lack of substantial northern hemispheric land ice outside of Greenland. We find that in 67%, 88% and 52% of the obliquity cycles during the early, middle and late Quaternary, respectively, a glacial termination is realized leading to irregular appearances of new interglacials during various parts of the last 2.6 Myr. This finding suggests that the proposed idea of terminations leading to new interglacials in the Quaternary as obliquity driven with growing influence of land ice volume on the timing of deglaciations during the last 1 Myr might be too simple. Alternatively, the land ice-based definition of interglacials needs revision if applied to the entire Quaternary.
Cathepsin D deficiency in mammary epithelium transiently stalls breast cancer by interference with mTORC1 signaling
Authors: Ketterer Stephanie , Mitschke Julia , Ketscher Anett , Schlimpert Manuel , Reichardt Wilfried , Baeuerle Natascha , Hess Maria Elena , Metzger Patrick , Boerries Melanie , Peters Christoph , Kammerer Bernd , Brummer Tilman , Steinberg Florian , Reinheckel Thomas 
Published: October 2020

AbstractCathepsin D (CTSD) is a lysosomal protease and a marker of poor prognosis in breast cancer. However, the cells responsible for this association and the function of CTSD in cancer are still incompletely understood. By using a conditional CTSD knockout mouse crossed to the transgenic MMTV-PyMT breast cancer model we demonstrate that CTSD deficiency in the mammary epithelium, but not in myeloid cells, blocked tumor development in a cell-autonomous manner. We show that lack of CTSD impaired mechanistic Target of Rapamycin Complex 1 (mTORC1) signaling and induced reversible cellular quiescence. In line, CTSD-deficient tumors started to grow with a two-month delay and quiescent Ctsd-/- tumor cells re-started proliferation upon long-term culture. This was accompanied by rewiring of oncogenic gene expression and signaling pathways, while mTORC1 signaling remained permanently disabled in CTSD-deficient cells. Together, these studies reveal a tumor cell-autonomous effect of CTSD deficiency, and establish a pivotal role of this protease in the cellular response to oncogenic stimuli.
Genome-wide RNAi screen for genes regulating glycolytic response to vemurafenib in BRAFV600 melanoma cells
Authors: Smith Lorey K. , Parmenter Tiffany , Gould Cathryn M. , Madhamshettiwar Piyush B. , Sheppard Karen E. , Simpson Kaylene J. , McArthur Grant A. 
Published: October 2020

AbstractIdentification of mechanisms underlying sensitivity and response to targeted therapies, such as the BRAF inhibitor vemurafenib, is critical in order to improve efficacy of these therapies in the clinic and delay onset of resistance. Glycolysis has emerged as a key feature of the BRAF inhibitor response in melanoma cells, and importantly, the metabolic response to vemurafenib in melanoma patients can predict patient outcome. Here, we present a multiparameter genome-wide siRNA screening dataset of genes that when depleted improve the viability and glycolytic response to vemurafenib in BRAFV600 mutated melanoma cells. These datasets are suitable for analysis of genes involved in cell viability and glycolysis in steady state conditions and following treatment with vemurafenib, as well as computational approaches to identify gene regulatory networks that mediate response to BRAF inhibition in melanoma.
Electricity from lignocellulosic substrates by thermophilic Geobacillus species
Authors: Shrestha Namita , Tripathi Abhilash Kumar , Govil Tanvi , Sani Rajesh Kumar , Urgun-Demirtas Meltem , Kasthuri Venkateswaran , Gadhamshetty Venkataramana 
Published: October 2020

AbstractGiven our vast lignocellulosic biomass reserves and the difficulty in bioprocessing them without expensive pretreatment and fuel separation steps, the conversion of lignocellulosic biomass directly into electricity would be beneficial. Here we report the previously unexplored capabilities of thermophilic Geobacillus sp. strain WSUCF1 to generate electricity directly from such complex substrates in microbial fuel cells. This process obviates the need for exogenous enzymes and redox mediator supplements. Cyclic voltammetry and chromatography studies revealed the electrochemical signatures of riboflavin molecules that reflect mediated electron transfer capabilities of strain WSUCF1. Proteomics and genomics analysis corroborated that WSUCF1 biofilms uses type-II NADH dehydrogenase and demethylmenaquinone methyltransferase to transfer the electrons to conducting anode via the redox active pheromone lipoproteins localized at the cell membrane.
Engineering and characterization of a novel Self Assembling Protein for Toxoplasma peptide vaccine in HLA-A*11:01, HLA-A*02:01 and HLA-B*07:02 transgenic mice
Authors: El Bissati Kamal , Zhou Ying , Paulillo Sara M. , Raman Senthil K. , Karch Christopher P. , Reed Steve , Estes Ashley , Estes Amber , Lykins Joseph , Burkhard Peter , McLeod Rima 
Published: October 2020

AbstractFighting smart diseases requires smart vaccines. Novel ways to present protective immunogenic peptide epitopes to human immune systems are needed. Herein, we focus on Self Assembling Protein Nanoparticles (SAPNs) as scaffolds/platforms for vaccine delivery that produce strong immune responses againstToxoplasma gondiiin HLA supermotif, transgenic mice. Herein, we present a useful platform to present peptides that elicit CD4+, CD8+T and B cell immune responses in a core architecture, formed by flagellin, administered in combination with TLR4 ligand-emulsion (GLA-SE) adjuvant. We demonstrate protection of HLA-A*11:01, HLA-A*02:01, and HLA-B*07:02 mice against toxoplasmosis by (i) this novel chimeric polypeptide, containing epitopes that elicit CD8+T cells,CD4+T helper cells, and IgG2b antibodies, and (ii) adjuvant activation of innate immune TLR4 and TLR5 pathways. HLA-A*11:01, HLA-A*02:01, and HLA-B*07:02q11 transgenic mouse splenocytes with peptides demonstrated predicted genetic restrictions. This creates a new paradigm-shifting vaccine approach to prevent toxoplasmosis, extendable to other diseases.
Shopper intent prediction from clickstream e-commerce data with minimal browsing information
Authors: Requena Borja , Cassani Giovanni , Tagliabue Jacopo , Greco Ciro , Lacasa Lucas 
Published: October 2020

AbstractWe address the problem of user intent prediction from clickstream data of an e-commerce website via two conceptually different approaches: a hand-crafted feature-based classification and a deep learning-based classification. In both approaches, we deliberately coarse-grain a new clickstream proprietary dataset to produce symbolic trajectories with minimal information. Then, we tackle the problem of trajectory classification of arbitrary length and ultimately, early prediction of limited-length trajectories, both for balanced and unbalanced datasets. Our analysis shows that k-gram statistics with visibility graph motifs produce fast and accurate classifications, highlighting that purchase prediction is reliable even for extremely short observation windows. In the deep learning case, we benchmarked previous state-of-the-art (SOTA) models on the new dataset, and improved classification accuracy over SOTA performances with our proposed LSTM architecture. We conclude with an in-depth error analysis and a careful evaluation of the pros and cons of the two approaches when applied to realistic industry use cases.
Bisindolylpyrrole triggers transient mitochondrial permeability transitions to cause apoptosis in a VDAC1/2 and cyclophilin D-dependent manner via the ANT-associated pore
Authors: Koushi Masami , Aoyama Yasunori , Kamei Yoshiko , Asakai Rei 
Published: October 2020

AbstractBisindolylpyrrole at 0.1 μM is cytoprotective in 2% FBS that is counteracted by cyclosporin-A (CsA), an inhibitor of cyclophilin-D (CypD). We hypothesized that the cytoprotective effect might be due to transient mitochondrial permeability transition (tPT). This study tested the hypothesis that bisindolylpyrrole can trigger tPT extensively, thereby leading to cell death under certain conditions. Indeed, CsA-sensitive tPT-mediated apoptosis could be induced by bisindolylpyrrole at > 5 μM in HeLa cells cultured in 0.1% FBS, depending on CypD and VDAC1/2, as shown by siRNA knockdown experiments. Rat liver mitochondria also underwent swelling in response to bisindolylpyrrole, which proceeded at a slower rate than Ca2+-induced swelling, and which was blocked by the VDAC inhibitor tubulin and the ANT inhibitor bongkrekate, indicating the involvement of the ANT-associated, smaller pore. We examined why 0.1% FBS is a prerequisite for apoptosis and found that apoptosis is blocked by PKC activation, which is counteracted by the overexpressed defective PKCε. In mitochondrial suspensions, bisindolylpyrrole triggered CsA-sensitive swelling, which was suppressed selectively by pretreatment with PKCε, but not in the co-presence of tubulin. These data suggest that upon PKC inactivation the cytoprotective compound bisindolylpyrrole can induce prolonged tPT causing apoptosis in a CypD-dependent manner through the VDAC1/2-regulated ANT-associated pore.