bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insights into the bioavailability of oceanic dissolved Fe from phytoplankton uptake kinetics
Authors: Shaked Yeala , Buck Kristen N , Mellett Travis , Maldonado Maria T 
Published: February 2020

Abstract
Phytoplankton growth in large parts of the world ocean is limited by low availability of dissolved iron (dFe), restricting oceanic uptake of atmospheric CO2. The bioavailability of dFe in seawater is however difficult to appraise since it is bound by a variety of poorly characterized organic ligands. Here, we propose a new approach for evaluating seawater dFe bioavailability based on its uptake rate constant by Fe-limited cultured phytoplankton. We utilized seven phytoplankton species of diverse classes, sizes, and provenances to probe for dFe bioavailability in 12 seawater samples from several ocean basins and depths. All tested phytoplankton acquired organically bound Fe in any given sample at similar rates (after normalizing to cellular surface area), confirming that multiple, Fe-limited phytoplankton species can be used to probe dFe bioavailability in seawater. These phytoplankton-based uptake rate constants allowed us to compare water types, and obtain a grand average estimate of seawater dFe bioavailability. Among water types, dFe bioavailability varied by approximately four-fold, and did not clearly correlate with Fe concentrations or any of the measured Fe speciation parameters. Compared with well-studied Fe complexes, seawater dFe is more available than model siderophore Fe, but less available than inorganic Fe. Exposure of seawater to sunlight, however, significantly enhanced dFe bioavailability. The rate constants established in this work, not only facilitate comparison between water types, but also allow calculation of Fe uptake rates by phytoplankton in the ocean based on measured dFe concentrations. The approach established and verified in this study, opens a new way for determining dFe bioavailability in samples across the ocean, and enables modeling of in situ Fe uptake rates by phytoplankton using dFe concentrations from GEOTRACES datasets.
TfR1 binding with H-ferritin nanocarrier achieves prognostic diagnosis and enhances the therapeutic efficacy in clinical gastric cancer
Authors: Cheng Xiaojing , Fan Kelong , Wang Lin , Ying Xiangji , Sanders Andrew J. , Guo Ting , Xing Xiaofang , Zhou Meng , Du Hong , Hu Ying , Ding Huirong , Li Ziyu , Wen Xianzi , Jiang Wenguo , Yan Xiyun , Ji Jiafu 
Published: February 2020

AbstractH-ferritin (HFn) nanocarrier is emerging as a promising theranostic platform for tumor diagnosis and therapy, which can specifically target tumor cells via binding transferrin receptor 1 (TfR1). This led us to investigate the therapeutic function of TfR1 in GC. The clinical significance of TfR1 was assessed in 178 GC tissues by using a magneto-HFn nanoparticle-based immunohistochemistry method. The therapeutic effects of doxorubicin-loaded HFn nanocarriers (HFn-Dox) were evaluated on TfR1-positive GC patient-derived xenograft (GC-PDX) models. The biological function of TfR1 was investigated through in vitro and in vivo assays. TfR1 was upregulated (73.03%) in GC tissues, and reversely correlated with patient outcome. TfR1-negative sorted cells exhibited tumor-initiating features, which enhanced tumor formation and migration/invasion, whereas TfR1-positive sorted cells showed significant proliferation ability. Knockout of TfR1 in GC cells also enhanced cell invasion. TfR1-deficient cells displayed immune escape by upregulating PD-L1, CXCL9, and CXCL10, when disposed with IFN-γ. Western blot results demonstrated that TfR1-knockout GC cells upregulated Akt and STAT3 signaling. Moreover, in TfR1-positive GC-PDX models, the HFn-Dox group significantly inhibited tumor growth, and increased mouse survival, compared with that of free-Dox group. TfR1 could be a potential prognostic and therapeutic biomarker for GC: (i) TfR1 reversely correlated with patient outcome, and its negative cells possessed tumor-aggressive features; (ii) TfR1-positive cells can be killed by HFn drug nanocarrier. Given the heterogeneity of GC, HFn drug nanocarrier combined with other therapies toward TfR1-negative cells (such as small molecules or immunotherapy) will be a new option for GC treatment.
Friendship paradox biases perceptions in directed networks
Authors: Alipourfard Nazanin , Nettasinghe Buddhika , Abeliuk Andrés , Krishnamurthy Vikram , Lerman Kristina 
Published: February 2020

AbstractSocial networks shape perceptions by exposing people to the actions and opinions of their peers. However, the perceived popularity of a trait or an opinion may be very different from its actual popularity. We attribute this perception bias to friendship paradox and identify conditions under which it appears. We validate the findings empirically using Twitter data. Within posts made by users in our sample, we identify topics that appear more often within users’ social feeds than they do globally among all posts. We also present a polling algorithm that leverages the friendship paradox to obtain a statistically efficient estimate of a topic’s global prevalence from biased individual perceptions. We characterize the polling estimate and validate it through synthetic polling experiments on Twitter data. Our paper elucidates the non-intuitive ways in which the structure of directed networks can distort perceptions and presents approaches to mitigate this bias.
Estimating growth patterns and driver effects in tumor evolution from individual samples
Authors: Salichos Leonidas , Meyerson William , Warrell Jonathan , Gerstein Mark 
Published: February 2020

AbstractTumors accumulate thousands of mutations, and sequencing them has given rise to methods for finding cancer drivers via mutational recurrence. However, these methods require large cohorts and underperform for low recurrence. Recently, ultra-deep sequencing has enabled accurate measurement of VAFs (variant-allele frequencies) for mutations, allowing the determination of evolutionary trajectories. Here, based solely on the VAF spectrum for an individual sample, we report on a method that identifies drivers and quantifies tumor growth. Drivers introduce perturbations into the spectrum, and our method uses the frequency of hitchhiking mutations preceding a driver to measure this. As validation, we use simulation models and 993 tumors from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium with previously identified drivers. Then we apply our method to an ultra-deep sequenced acute myeloid leukemia (AML) tumor and identify known cancer genes and additional driver candidates. In summary, our framework presents opportunities for personalized driver diagnosis using sequencing data from a single individual.
MTR4 drives liver tumorigenesis by promoting cancer metabolic switch through alternative splicing
Authors: Yu Lili , Kim Jinchul , Jiang Lei , Feng Bingbing , Ying Yue , Ji Kai-yuan , Tang Qingshuang , Chen Wancheng , Mai Taoyi , Dou Wenlong , Zhou Jianlong , Xiang Le-yang , He Yang-fan , Yang Dinghua , Li Qingjiao , Fu Xuemei , Xu Yang 
Published: February 2020

AbstractThe metabolic switch from oxidative phosphorylation to glycolysis is required for tumorigenesis in order to provide cancer cells with energy and substrates of biosynthesis. Therefore, it is important to elucidate mechanisms controlling the cancer metabolic switch. MTR4 is a RNA helicase associated with a nuclear exosome that plays key roles in RNA processing and surveillance. We demonstrate that MTR4 is frequently overexpressed in hepatocellular carcinoma (HCC) and is an independent diagnostic marker predicting the poor prognosis of HCC patients. MTR4 drives cancer metabolism by ensuring correct alternative splicing of pre-mRNAs of critical glycolytic genes such as GLUT1 and PKM2. c-Myc binds to the promoter of the MTR4 gene and is important for MTR4 expression in HCC cells, indicating that MTR4 is a mediator of the functions of c-Myc in cancer metabolism. These findings reveal important roles of MTR4 in the cancer metabolic switch and present MTR4 as a promising therapeutic target for treating HCC.
Initiation of a stable convective hydroclimatic regime in Central America circa 9000 years BP
Authors: Winter Amos , Zanchettin Davide , Lachniet Matthew , Vieten Rolf , Pausata Francesco S. R. , Ljungqvist Fredrik Charpentier , Cheng Hai , Edwards R. Lawrence , Miller Thomas , Rubinetti Sara , Rubino Angelo , Taricco Carla 
Published: February 2020

AbstractMany Holocene hydroclimate records show rainfall changes that vary with local orbital insolation. However, some tropical regions display rainfall evolution that differs from gradual precessional pacing, suggesting that direct rainfall forcing effects were predominantly driven by sea-surface temperature thresholds or inter-ocean temperature gradients. Here we present a 12,000 yr continuous U/Th-dated precipitation record from a Guatemalan speleothem showing that Central American rainfall increased within a 2000 yr period from a persistently dry state to an active convective regime at 9000 yr BP and has remained strong thereafter. Our data suggest that the Holocene evolution of Central American rainfall was driven by exceeding a temperature threshold in the nearby tropical oceans. The sensitivity of this region to slow changes in radiative forcing is thus strongly mediated by internal dynamics acting on much faster time scales.
Genetic influence is linked to cortical morphology in category-selective areas of visual cortex
Authors: Abbasi Nooshin , Duncan John , Rajimehr Reza 
Published: February 2020

AbstractHuman visual cortex contains discrete areas that respond selectively to specific object categories such as faces, bodies, and places. A long-standing question is whether these areas are shaped by genetic or environmental factors. To address this question, here we analyzed functional MRI data from an unprecedented number (n = 424) of monozygotic (MZ) and dizygotic (DZ) twins. Category-selective maps were more identical in MZ than DZ twins. Within each category-selective area, distinct subregions showed significant genetic influence. Structural MRI analysis revealed that the ‘genetic voxels’ were predominantly located in regions with higher cortical curvature (gyral crowns in face areas and sulcal fundi in place areas). Moreover, we found that cortex was thicker and more myelinated in genetic voxels of face areas, while it was thinner and less myelinated in genetic voxels of place areas. This double dissociation suggests a differential development of face and place areas in cerebral cortex.
Experimental evidence of long-term oceanic circulation reversals without wind influence in the North Ionian Sea
Authors: Rubino Angelo , Gačić Miroslav , Bensi Manuel , Kovačević Vedrana , Malačič Vlado , Menna Milena , Negretti Maria Eletta , Sommeria Joël , Zanchettin Davide , Barreto Ricardo V. , Ursella Laura , Cardin Vanessa , Civitarese Giuseppe , Orlić Mirko , Petelin Boris , Siena Giuseppe 
Published: February 2020

AbstractUnder the emerging features of interannual-to-decadal ocean variability, the periodical reversals of the North Ionian Gyre (NIG), driven mostly by the mechanism named Adriatic-Ionian Bimodal Oscillating System (BiOS), are known as impacting on marine physics and biogeochemistry and potentially influencing short-term regional climate predictability in the Eastern Mediterranean. Whilst it has been suggested that local wind forcing cannot explain such variability, aspects of the alternative hypothesis indicating that NIG reversals mainly arises from an internal ocean feedback mechanism alone remain largely debated. Here we demonstrate, using the results of physical experiments, performed in the world’s largest rotating tank and numerical simulations, that the main observed feature of BiOS, i.e., the switch of polarity of the near-surface circulation in the NIG, can be induced by a mere injection of dense water on a sloping bottom. Hence, BiOS is a truly oceanic mode of variability and abrupt polarity changes in circulation can arise solely from extreme dense water formation events.
Relative Average Look Duration and its Association with Neurophysiological Activity in Young Children with Autism Spectrum Disorder
Authors: Isaev Dmitry Yu. , Major Samantha , Murias Michael , Carpenter Kimberly L. H. , Carlson David , Sapiro Guillermo , Dawson Geraldine 
Published: February 2020

AbstractAutism Spectrum Disorder (ASD) is characterized by early attentional differences that often precede the hallmark symptoms of social communication impairments. Development of novel measures of attentional behaviors may lead to earlier identification of children at risk for ASD. In this work, we first introduce a behavioral measure, Relative Average Look Duration (RALD), indicating attentional preference to different stimuli, such as social versus nonsocial stimuli; and then study its association with neurophysiological activity. We show that (1) ASD and typically developing (TD) children differ in both (absolute) Average Look Duration (ALD) and RALD to stimuli during an EEG experiment, with the most pronounced differences in looking at social stimuli; and (2) associations between looking behaviors and neurophysiological activity, as measured by EEG, are different for children with ASD versus TD. Even when ASD children show attentional engagement to social content, our results suggest that their underlying brain activity is different than TD children. This study therefore introduces a new measure of social/nonsocial attentional preference in ASD and demonstrates the value of incorporating attentional variables measured simultaneously with EEG into the analysis pipeline.
Tissue-specific promoter-based reporter system for monitoring cell differentiation from iPSCs to cardiomyocytes
Authors: Fiedorowicz Katarzyna , Rozwadowska Natalia , Zimna Agnieszka , Malcher Agnieszka , Tutak Katarzyna , Szczerbal Izabela , Nowicka-Bauer Karolina , Nowaczyk Magdalena , Kolanowski Tomasz J. , Łabędź Wojciech , Kubaszewski Łukasz , Kurpisz Maciej 
Published: February 2020

AbstractThe possibility of using stem cell-derived cardiomyocytes opens a new platform for modeling cardiac cell differentiation and disease or the development of new drugs. Progress in this field can be accelerated by high-throughput screening (HTS) technology combined with promoter reporter system. The goal of the study was to create and evaluate a responsive promoter reporter system that allows monitoring of iPSC differentiation towards cardiomyocytes. The lentiviral promoter reporter system was based ontroponin 2(TNNT2) andalpha cardiac actin(ACTC) with firefly luciferase and mCherry, respectively. The system was evaluated in twoin vitromodels. First, system followed the differentiation ofTNNT2-luc-T2A-Puro-mCMV-GFP and hACTC-mcherry-WPRE-EF1-Neofrom transduced iPSC line towards cardiomyocytes and revealed the significant decrease in both inserts copy number during the prolongedin vitrocell culture (confirmed by I-FISH, ddPCR, qPCR). Second, differentiated and contracting control cardiomyocytes (obtained from control non-reporter transduced iPSCs) were subsequently transduced withTNNT2-luc-T2A-Puro-CMV-GFP and hACTC-mcherry-WPRE-EF1-Neolentiviruses to observe the functionality of obtained cardiomyocytes. Our results indicated that the reporter modified cell lines can be used for HTS applications, but it is essential to monitor the stability of the reporter sequence during extended cellin vitroculture.
Effects of Rikkunshito treatment on renal fibrosis/inflammation and body weight reduction in a unilateral ureteral obstruction model in mice
Authors: Wakui Hiromichi , Yamaji Takahiro , Azushima Kengo , Uneda Kazushi , Haruhara Kotaro , Nakamura Akiko , Ohki Kohji , Kinguchi Sho , Kobayashi Ryu , Urate Shingo , Suzuki Toru , Kamimura Daisuke , Minegishi Shintaro , Ishigami Tomoaki , Kanaoka Tomohiko , Matsuo Kohei , Miyazaki Tomoyuki , Fujikawa Tetsuya , Yamashita Akio , Tamura Kouichi 
Published: February 2020

AbstractChronic kidney disease (CKD) progresses to end-stage renal failure via renal tubulointerstitial fibrosis. Malnutrition, inflammation, and arteriosclerosis interact to exacerbate the poor prognosis of CKD, and their effective management is thus essential. The traditional Japanese medicine Rikkunshito (RKT) exerts appetite-stimulating effects via ghrelin, which attenuates inflammation and fibrosis. We evaluated the therapeutic effect of RKT in unilateral ureter obstruction (UUO)-induced renal fibrosis/inflammation and body weight loss in mice. UUO and sham-operated mice were fed a standard diet or diet containing 3.0% RKT. Renal fibrosis was investigated by histopathology and macrophage infiltration was determined by immunohistochemistry. Expression levels of genes associated with fibrosis, inflammation, ghrelin, and mitochondrial function were determined by quantitative reverse transcription-polymerase chain reaction and western blot analyses. RKT treatment partially prevented UUO-induced weight loss but failed to attenuate renal fibrosis and inflammation. Renal expression of sirtuin 1, a ghrelin-downstream signalling molecule, and gene expression of peroxisome proliferator-activated receptor-γ coactivator 1α and Bcl-2/adenovirus E1B interacting protein 3 were unaffected by RKT. These results indicate that RKT inhibits weight loss but does not improve renal fibrosis or inflammation in a rapidly progressive renal fibrosis mouse model. RKT may have a protective effect on weight loss associated with CKD.
Two dimensional (2D) reduced graphene oxide (RGO)/hexagonal boron nitride (h-BN) based nanocomposites as anodes for high temperature rechargeable lithium-ion batteries
Authors: Mussa Yasmin , Ahmed Faheem , Arsalan Muhammad , Alsharaeh Edreese 
Published: February 2020

AbstractWith lithium-ion (li-ion) batteries as energy storage devices, operational safety from thermal runaway remains a major obstacle especially for applications in harsh environments such as in the oil industry. In this approach, a facile method via microwave irradiation technique (MWI) was followed to prepare Co3O4/reduced graphene oxide (RGO)/hexagonal boron nitride (h-BN) nanocomposites as anodes for high temperature li-ion batteries. Results showed that the addition ofh-BN not only enhanced the thermal stability of Co3O4/RGO nanocomposites but also enhanced the specific surface area. Co3O4/RGO/h-BN nanocomposites displayed the highest specific surface area of 191 m2/g evidencing the synergistic effects between RGO andh-BN. Moreover, Co3O4/RGO/h-BN also displayed the highest specific capacity with stable reversibility on the high performance after 100 cycles and lower internal resistance. Interestingly, this novel nanocomposite exhibits outstanding high temperature performances with excellent cycling stability (100% capacity retention) and a decreased internal resistance at 150 °C.
Numerical simulation of the flow and erosion behavior of exhaust gas and particles in polysilicon reduction furnace
Authors: Qili Wang , Binbin Jia , Mingquan Yu , Min He , Xiaochuan Li , Komarneni Sridhar 
Published: February 2020

AbstractIn order to study the flow and erosion behavior of gas-solid exhaust in the polysilicon reduction furnace, the flow characteristics of exhaust gas and silicon particles were analyzed. The flow model and erosion model of exhaust gas and silicon particles were established based on the gas-solid flow theory and the erosion theory. The erosion and wear behavior of the gas-solid mixture in the flow passage pipeline were studied by numerical simulation. The results show that the wear and erosion from Nos. 1 to 8 regions at the bottom of the ring were caused by silicon particles colliding with high angle. The wear and erosion of 2 regions from Nos. 9 to 10 at the outside of the up azimuth on both sides of loop pipe outlets, 4 regions from Nos. 11 to 14 on the upper and lower wall of single furnace main channel were severely affected wear regions, which is caused by silicon particles with low angle and high velocity. Through comparative analysis, the erosion of upper wall of single furnace main channel is most serious. Increased gas velocity, particle concentration and particle size will exacerbate the erosion and wear rate of the pipeline in polysilicon reduction furnace, but the distribution and development of severe wear zone would not be affected significantly.
Role of the imprinted allele of the Cdkn1c gene in mouse neocortical development
Authors: Imaizumi Yui , Furutachi Shohei , Watanabe Tomoyuki , Miya Hiroaki , Kawaguchi Daichi , Gotoh Yukiko 
Published: February 2020

AbstractImprinted genes are expressed from only one allele in a parent of origin–specific manner. The cyclin-dependent kinase inhibitor p57kip2 is encoded by an imprinted gene Cdkn1c, with the paternal allele being silenced. The possible expression and function of the paternal allele of Cdkn1c have remained little studied, however. We now show that the paternal allele of the Cdkn1c gene is expressed at a low level in the developing mouse neocortex. Surprisingly, the central nervous system-specific conditional deletion of the paternal allele (pat cKO) at the Cdkn1c locus resulted in a marked reduction in brain size. Furthermore, pat cKO gradually reduced the number of neural stem-progenitor cells (NPCs) during neocortical development, and thus reduced the number of upper-layer neurons, which were derived from late-stage NPCs. Our results thus show that the paternal allele of the Cdkn1c locus plays a key role in maintenance of NPCs during neocortical development.
ASK1 promotes uterine inflammation leading to pathological preterm birth
Authors: Yoshikawa Midori , Iriyama Takayuki , Suzuki Kensuke , Sayama Seisuke , Tsuruga Tetsushi , Kumasawa Keiichi , Nagamatsu Takeshi , Homma Kengo , Naguro Isao , Osuga Yutaka , Ichijo Hidenori , Fujii Tomoyuki 
Published: February 2020

AbstractIt is widely accepted that enhanced uterine inflammation associated with microbial infection is a main causative factor for preterm birth. However, little is known about the molecular basis by which inflammation is associated with preterm birth. Here, we demonstrate that apoptosis signal-regulating kinase 1 (ASK1), a member of the mitogen-activated protein 3-kinase family, facilitates inflammation-induced preterm birth and that inhibition of ASK1 activity is sufficient to suppress preterm birth. ASK1-deficient pregnant mice exhibited reduced incidence of lipopolysaccharide (LPS)-induced preterm birth. ASK1 was required for the induction of LPS-induced inflammatory responses related to preterm birth, including pro-inflammatory cytokine production in the uterus and peritoneal cavities. In addition, selective suppression of uterine ASK1 activity through a chemical genetic approach reduced the incidence of LPS-induced preterm birth. Moreover, translational studies with human choriodecidua demonstrated that ASK1 was required for LPS-induced activation of JNK and p38 and pro-inflammatory cytokine production. Our findings suggest that ASK1 activation is responsible for the induction of inflammation that leads to preterm birth and that the blockade of ASK1 signaling might be a promising therapeutic target for preventing preterm birth.