bluuebunny/crossref_metadata_2025_split huggingface dataset:
Time-lapse single-cell transcriptomics reveals modulation of histone H3 for dormancy breaking in fission yeast
Authors: Tsuyuzaki Hayato , Hosokawa Masahito , Arikawa Koji , Yoda Takuya , Okada Naoyuki , Takeyama Haruko , Sato Masamitsu 
Published: March 2020

AbstractHow quiescent cells break dormancy is a key issue in eukaryotic cells including cancer. Fungal spores, for example, remain quiescent for long periods until nourished, although the mechanisms by which dormancy is broken remain enigmatic. Transcriptome analysis could provide a clue, but methods to synchronously germinate large numbers of spores are lacking, and thus it remains a challenge to analyse gene expression upon germination. Hence, we develop methods to assemble transcriptomes from individual, asynchronous spore cells of fission yeast undergoing germination to assess transcriptomic changes over time. The virtual time-lapse analyses highlights one of three copies of histone H3 genes whose transcription fluctuates during the initial stage of germination. Disruption of this temporal fluctuation causes defects in spore germination despite no visible defects in other stages of the life cycle. We conclude that modulation of histone H3 expression is a crucial ‘wake-up’ trigger at dormancy breaking.
Fresh groundwater discharge insignificant for the world’s oceans but important for coastal ecosystems
Authors: Luijendijk Elco , Gleeson Tom , Moosdorf Nils 
Published: March 2020

AbstractThe flow of fresh groundwater may provide substantial inputs of nutrients and solutes to the oceans. However, the extent to which hydrogeological parameters control groundwater flow to the world’s oceans has not been quantified systematically. Here we present a spatially resolved global model of coastal groundwater discharge to show that the contribution of fresh groundwater accounts for ~0.6% (0.004%–1.3%) of the total freshwater input and ~2% (0.003%–7.7%) of the solute input for carbon, nitrogen, silica and strontium. However, the coastal discharge of fresh groundwater and nutrients displays a high spatial variability and for an estimated 26% (0.4%–39%) of the world’s estuaries, 17% (0.3%–31%) of the salt marshes and 14% (0.1–26%) of the coral reefs, the flux of terrestrial groundwater exceeds 25% of the river flux and poses a risk for pollution and eutrophication.
First draft genome for the sand-hopper Trinorchestia longiramus
Authors: Patra Ajit Kumar , Chung Oksung , Yoo Ji Yong , Kim Min Seop , Yoon Moon Geun , Choi Jeong-Hyeon , Yang Youngik 
Published: March 2020

AbstractCrustacean amphipods are important trophic links between primary producers and higher consumers. Although most amphipods occur in or around aquatic environments, the family Talitridae is the only family found in terrestrial and semi-terrestrial habitats. The sand-hopper Trinorchestia longiramus is a talitrid species often found in the sandy beaches of South Korea. In this study, we present the first draft genome assembly and annotation of this species. We generated ~380.3 Gb of sequencing data assembled in a 0.89 Gb draft genome. Annotation analysis estimated 26,080 protein-coding genes, with 89.9% genome completeness. Comparison with other amphipods showed that T. longiramus has 327 unique orthologous gene clusters, many of which are expanded gene families responsible for cellular transport of toxic substances, homeostatic processes, and ionic and osmotic stress tolerance. This first talitrid genome will be useful for further understanding the mechanisms of adaptation in terrestrial environments, the effects of heavy metal toxicity, as well as for studies of comparative genomic variation across amphipods.
Comprehensive analyses of the annexin (ANN) gene family in Brassica rapa, Brassica oleracea and Brassica napus reveals their roles in stress response
Authors: He Xin , Liao Li , Xie Sai , Yao Min , Xie Pan , Liu Wei , Kang Yu , Huang Luyao , Wang Mei , Qian Lunwen , Liu Zhongsong , Guan Chunyun , Guan Mei , Hua Wei 
Published: March 2020

AbstractAnnexins (ANN) are a multigene, evolutionarily conserved family of calcium-dependent and phospholipid-binding proteins that play important roles in plant development and stress resistance. However, a systematic comprehensive analysis of ANN genes of Brassicaceae species (Brassica rapa, Brassica oleracea, and Brassica napus) has not yet been reported. In this study, we identified 13, 12, and 26 ANN genes in B. rapa, B. oleracea, and B. napus, respectively. About half of these genes were clustered on various chromosomes. Molecular evolutionary analysis showed that the ANN genes were highly conserved in Brassicaceae species. Transcriptome analysis showed that different group ANN members exhibited varied expression patterns in different tissues and under different (abiotic stress and hormones) treatments. Meanwhile, same group members from Arabidopsis thaliana, B. rapa, B. oleracea, and B. napus demonstrated conserved expression patterns in different tissues. The weighted gene coexpression network analysis (WGCNA) showed that BnaANN genes were induced by methyl jasmonate (MeJA) treatment and played important roles in jasmonate (JA) signaling and multiple stress response in B. napus.
Hypoxia sensing by hepatic stellate cells leads to VEGF-dependent angiogenesis and may contribute to accelerated liver regeneration
Authors: Dirscherl Konstantin , Schläpfer Martin , Roth Z’graggen Birgit , Wenger Roland H , Booy Christa , Flury-Frei Renata , Fatzer Rita , Aloman Costica , Bartosch Birke , Parent Romain , Kurtcuoglu Vartan , de Zélicourt Diane , Spahn Donat R. , Beck Schimmer Beatrice , Schadde Erik 
Published: March 2020

AbstractPortal vein ligation (PVL) induces liver growth prior to resection. Associating liver partition and portal vein ligation (PVL plus transection=ALPPS) or the addition of the prolyl-hydroxylase inhibitor dimethyloxalylglycine (DMOG) to PVL both accelerate growth via stabilization of HIF-α subunits. This study aims at clarifying the crosstalk of hepatocytes (HC), hepatic stellate cells (HSC) and liver sinusoidal endothelial cells (LSEC) in accelerated liver growth. In vivo, liver volume, HC proliferation, vascular density and HSC activation were assessed in PVL, ALPPS, PVL+DMOG and DMOG alone. Proliferation of HC, HSC and LSEC was determined under DMOG in vitro. Conditioned media experiments of DMOG-exposed cells were performed. ALPPS and PVL+DMOG accelerated liver growth and HC proliferation in comparison to PVL. DMOG alone did not induce HC proliferation, but led to increased vascular density, which was also observed in ALPPS and PVL+DMOG. Activated HSC were detected in ALPPS, PVL+DMOG and DMOG, again not in PVL. In vitro, DMOG had no proliferative effect on HC, but conditioned supernatant of DMOG-treated HSC induced VEGF-dependent proliferation of LSEC. Transcriptome analysis confirmed activation of proangiogenic factors in hypoxic HSC. Hypoxia signaling in HSC induces VEGF-dependent angiogenesis. HSC play a crucial role in the cellular crosstalk of rapid liver regeneration.
Modifiable risk factors for 9-year mortality in older English and Brazilian adults: The ELSA and SIGa-Bagé ageing cohorts
Authors: Kessler Marciane , Thumé Elaine , Scholes Shaun , Marmot Michael , Facchini Luiz Augusto , Nunes Bruno Pereira , Machado Karla Pereira , Soares Mariangela Uhlmann , de Oliveira Cesar 
Published: March 2020

AbstractTo quantify and compare 9-year all-cause mortality risk attributable to modifiable risk factors among older English and Brazilian adults. We used data for participants aged 60 years and older from the English Longitudinal Study of Ageing (ELSA) and the Bagé Cohort Study of Ageing (SIGa-Bagé). The five modifiable risk factors assessed at baseline were smoking, hypertension, diabetes, obesity and physical inactivity. Deaths were identified through linkage to mortality registers. For each risk factor, estimated all-cause mortality hazard ratios (HR) and population attributable fractions (PAF) were adjusted by age, sex, all other risk factors and socioeconomic position (wealth) using Cox proportional hazards modelling. We also quantified the risk factor adjusted wealth gradients in mortality, by age and sex. Among the participants, 659 (ELSA) and 638 (SIGa-Bagé) died during the 9-year follow-up. Mortality rates were higher in SIGa-Bagé. HRs and PAFs showed more similarities than differences, with physical inactivity (PAF 16.5% ELSA; 16.7% SIGa-Bagé) and current smoking (PAF 4.9% for both cohorts) having the strongest association. A clear graded relationship existed between the number of risk factors and subsequent mortality. Wealth gradients in mortality were apparent in both cohorts after full adjustment, especially among men aged 60–74 in ELSA. A different pattern was found among older women, especially in SIGa-Bagé. These findings call attention for the challenge to health systems to prevent and modify the major risk factors related to non-communicable diseases, especially physical inactivity and smoking. Furthermore, wealth inequalities in mortality persist among older adults.
APOE4 is Associated with Differential Regional Vulnerability to Bioenergetic Deficits in Aged APOE Mice
Authors: Area-Gomez Estela , Larrea Delfina , Pera Marta , Agrawal Rishi R. , Guilfoyle David N. , Pirhaji Leila , Shannon Kathleen , Arain Hirra A. , Ashok Archana , Chen Qiuying , Dillman Allissa A. , Figueroa Helen Y. , Cookson Mark R. , Gross Steven S. , Fraenkel Ernest , Duff Karen E. , Nuriel Tal 
Published: March 2020

AbstractThe ε4 allele of apolipoprotein E (APOE) is the dominant genetic risk factor for late-onset Alzheimer’s disease (AD). However, the reason for the association between APOE4 and AD remains unclear. While much of the research has focused on the ability of the apoE4 protein to increase the aggregation and decrease the clearance of Aβ, there is also an abundance of data showing that APOE4 negatively impacts many additional processes in the brain, including bioenergetics. In order to gain a more comprehensive understanding of APOE4′s role in AD pathogenesis, we performed a transcriptomics analysis of APOE4 vs. APOE3 expression in the entorhinal cortex (EC) and primary visual cortex (PVC) of aged APOE mice. This study revealed EC-specific upregulation of genes related to oxidative phosphorylation (OxPhos). Follow-up analysis utilizing the Seahorse platform showed decreased mitochondrial respiration with age in the hippocampus and cortex of APOE4 vs. APOE3 mice, but not in the EC of these mice. Additional studies, as well as the original transcriptomics data, suggest that multiple bioenergetic pathways are differentially regulated by APOE4 expression in the EC of aged APOE mice in order to increase the mitochondrial coupling efficiency in this region. Given the importance of the EC as one of the first regions to be affected by AD pathology in humans, the observation that the EC is susceptible to differential bioenergetic regulation in response to a metabolic stressor such as APOE4 may point to a causative factor in the pathogenesis of AD.
Melinjo seed extract increases adiponectin multimerization in physiological and pathological conditions
Authors: Oniki Kentaro , Kawakami Taisei , Nakashima Azusa , Miyata Keishi , Watanabe Takehisa , Fujikawa Haruka , Nakashima Ryunosuke , Nasu Aoi , Eto Yuka , Takahashi Noriki , Nohara Hirofumi , Suico Mary Ann , Kotani Shunsuke , Obata Yui , Sakamoto Yuki , Seguchi Yuri , Saruwatari Junji , Imafuku Tadashi , Watanabe Hiroshi , Maruyama Toru , Kai Hirofumi , Shuto Tsuyoshi 
Published: March 2020

AbstractMelinjo seed extract (MSE) contains large amounts of polyphenols, including dimers of trans-resveratrol (e.g. gnetin C, L, gnemonoside A, B and D), and has been shown to potentially improve obesity. However, there is no clinical evidence regarding the anti-obesity effects of MSE, and its mechanisms are also unclear. We investigated the hypothesis that MSE supplementation increases the adiponectin (APN) multimerization via the up-regulation of disulfide bond A oxidoreductase-like protein (DsbA-L) under either or both physiological and obese conditions. To investigate the effect of MSE on the physiological condition, 42 healthy young volunteers were enrolled in a randomized, double-blind placebo-controlled clinical trial for 14 days. The participants were randomly assigned to the MSE 150 mg/day, MSE 300 mg/day or placebo groups. Furthermore, in order to investigate the effect of MSE on APN levels under obese conditions, we administered MSE powder (500 or 1000 mg/kg/day) to control-diet- or high-fat-diet (HFD)-fed C57BL/6 mice for 4 weeks. All participants completed the clinical trial. The administration of MSE 300 mg/day was associated with an increase in the ratio of HMW/total APN in relation to the genes regulating APN multimerization, including DsbA-L. Furthermore, this effect of MSE was more pronounced in carriers of the DsbA-L rs191776 G/T or T/T genotype than in others. In addition, the administration of MSE to HFD mice suppressed their metabolic abnormalities (i.e. weight gain, increased blood glucose level and fat mass accumulation) and increased the levels of total and HMW APN in serum and the mRNA levels of ADIPOQ and DsbA-L in adipose tissue. The present study suggests that MSE may exert beneficial effects via APN multimerization in relation to the induction of DsbA-L under both physiological and obese conditions.
Bridging substrate intake kinetics and bacterial growth phenotypes with flux balance analysis incorporating proteome allocation
Authors: Zeng Hong , Yang Aidong 
Published: March 2020

AbstractEmpirical kinetic models such as the Monod equation have been widely applied to relate the cell growth with substrate availability. The Monod equation shares a similar form with the mechanistically-based Michaelis-Menten kinetics for enzymatic processes, which has provoked long-standing and un-concluded conjectures on their relationship. In this work, we integrated proteome allocation principles into a Flux Balance Analysis (FBA) model of Escherichia coli, which quantitatively revealed potential mechanisms that underpin the phenomenological Monod parameters: the maximum specific growth rate could be dictated by the abundance of growth-controlling proteome and growth-pertinent proteome cost; more importantly, the Monod constant (Ks) was shown to relate to the Michaelis constant for substrate transport (Km,g), with the link being dependent on the cell’s metabolic strategy. Besides, the proposed model was able to predict glucose uptake rate at given external glucose concentration through the size of available proteome resource for substrate transport and its enzymatic cost, while growth rate and acetate overflow were accurately simulated for two E. coli strains. Bridging the enzymatic kinetics of substrate intake and overall growth phenotypes, this work offers a mechanistic interpretation to the empirical Monod law, and demonstrates the potential of coupling local and global cellular constrains in predictive modelling.
Combined behavioral and electrophysiological evidence for a direct cortical effect of prefrontal tDCS on disorders of consciousness
Authors: Hermann Bertrand , Raimondo Federico , Hirsch Lukas , Huang Yu , Denis-Valente Mélanie , Pérez Pauline , Engemann Denis , Faugeras Frédéric , Weiss Nicolas , Demeret Sophie , Rohaut Benjamin , Parra Lucas C. , Sitt Jacobo D. , Naccache Lionel 
Published: March 2020

AbstractSevere brain injuries can lead to long-lasting disorders of consciousness (DoC) such as vegetative state/unresponsive wakefulness syndrome (VS/UWS) or minimally conscious state (MCS). While behavioral assessment remains the gold standard to determine conscious state, EEG has proven to be a promising complementary tool to monitor the effect of new therapeutics. Encouraging results have been obtained with invasive electrical stimulation of the brain, and recent studies identified transcranial direct current stimulation (tDCS) as an effective approach in randomized controlled trials. This non-invasive and inexpensive tool may turn out to be the preferred treatment option. However, its mechanisms of action and physiological effects on brain activity remain unclear and debated. Here, we stimulated 60 DoC patients with the anode placed over left-dorsolateral prefrontal cortex in a prospective open-label study. Clinical behavioral assessment improved in twelve patients (20%) and none deteriorated. This behavioral response after tDCS coincided with an enhancement of putative EEG markers of consciousness: in comparison with non-responders, responders showed increases of power and long-range cortico-cortical functional connectivity in the theta-alpha band, and a larger and more sustained P300 suggesting improved conscious access to auditory novelty. The EEG changes correlated with electric fields strengths in prefrontal cortices, and no correlation was found on the scalp. Taken together, this prospective intervention in a large cohort of DoC patients strengthens the validity of the proposed EEG signatures of consciousness, and is suggestive of a direct causal effect of tDCS on consciousness.
Preparation of macroporous transition metal hydroxide monoliths via a sol-gel process accompanied by phase separation
Authors: Liu Fu , Feng Daoyan , Yang Hui , Guo Xingzhong 
Published: March 2020

AbstractThree-dimensional transition metal hydroxide monoliths were facilely fabricated by a sol-gel process accompanied by phase separation in the presence of polyacrylic acid (PAA) and propylene oxide (PO). In the typical ZnCl2-PAA-PO system, PAA is used as a phase separation inducer as well as a framework former to control the phase separation and the formation of macrostructures, whereas PO works as a proton scavenger to initiate the gelation of the system and freeze the macrostructures. Appropriate amount of PAA, PO and solvents allow the formation of zinc (Zn) hydroxide monolith with cocontinuous skeletons and interconnected macropores, and the construction mechanism and characteristics of macrostructure are also investigated. The resultant dried gels are amorphous Zn hydroxide monolith with a narrow macropore size distribution (~1 μm). This approach is further used to successfully prepare macroporous single or binary composite transition metal hydroxide monoliths.
Genome-based Salmonella serotyping as the new gold standard
Authors: Banerji Sangeeta , Simon Sandra , Tille Andreas , Fruth Angelika , Flieger Antje 
Published: March 2020

AbstractSalmonella enterica is the second most reported bacterial cause of food-borne infections in Europe. Therefore molecular surveillance activities based on pathogen subtyping are an important measure of controlling Salmonellosis by public health agencies. In Germany, at the federal level, this work is carried out by the National Reference Center for Salmonella and other Bacterial Enteric Pathogens (NRC). With rise of next generation sequencing techniques, the NRC has introduced whole-genome-based typing methods for S. enterica in 2016. In this study we report on the feasibility of genome-based in silico serotyping in the German setting using raw sequence reads. We found that SeqSero and seven gene MLST showed 98% and 95% concordance, respectively, with classical serotyping for the here evaluated serotypes, including the most common German serotypes S. Enteritidis and S. Typhimurium as well as less frequently found serotypes. The level of concordance increased to >99% when the results of both in silico methods were combined. However, both tools exhibited misidentification of monophasic variants, in particular monophasic S. Typhimurium and therefore need to be fine-tuned for reliable detection of this epidemiologically important variant. We conclude that with adjustments Salmonella genome-based serotyping might become the new gold standard.
Signals of anticipation of reward and of mean reward rates in the human brain
Authors: Viviani Roberto , Dommes Lisa , Bosch Julia , Steffens Michael , Paul Anna , Schneider Katharina L. , Stingl Julia C. , Beschoner Petra 
Published: March 2020

AbstractTheoretical models of dopamine function stemming from reinforcement learning theory have emphasized the importance of prediction errors, which signal changes in the expectation of impending rewards. Much less is known about the effects of mean reward rates, which may be of motivational significance due to their role in computing the optimal effort put into exploiting reward opportunities. Here, we used a reinforcement learning model to design three functional neuroimaging studies and disentangle the effects of changes in reward expectations and mean reward rates, showing recruitment of specific regions in the brainstem regardless of prediction errors. While changes in reward expectations activated ventral striatal areas as in previous studies, mean reward rates preferentially modulated the substantia nigra/ventral tegmental area, deep layers of the superior colliculi, and a posterior pontomesencephalic region. These brainstem structures may work together to set motivation and attentional efforts levels according to perceived reward opportunities.
Dasatinib exacerbates splenomegaly of mice inoculated with Epstein-Barr virus-infected lymphoblastoid cell lines
Authors: Kotaki Ryutaro , Kawashima Masaharu , Yamamoto Yuichiro , Higuchi Hiroshi , Nagashima Etsuko , Kurosaki Natsumi , Takamatsu Masako , Kikuti Yara Yukie , Imadome Ken-Ichi , Nakamura Naoya , Kotani Ai 
Published: March 2020

AbstractLatent infection of Epstein-Barr virus (EBV) is associated with a poor prognosis in patients with B cell malignancy. We examined whether dasatinib, a multi kinase inhibitor, which is broadly used for chronic myeloid leukemia and Philadelphia chromosome-positive acute lymphoblastic leukemia is effective on EBV-positive B cell malignancies, using lymphoblastoid cell lines (LCLs) in vitro and in vivo. As a result, in vitro experiments showed that dasatinib induced cell death of the EBV-LCLs which was not accompanied with a lytic reactivation of EBVs. To evaluate the effectiveness in EBV latency type III represented by immunodeficiency lymphoma, LCL-inoculated immunodeficient NOD/shi-scid/Il2rgnul (NOG) mice were treated with dasatinib. However, in vivo experiments revealed that dasatinib treatment exacerbated tumor cell infiltration into the spleen of LCL-inoculated NOG mice, whereas tumor size at the inoculated site was not affected by the treatment. These results suggest that dasatinib exacerbates the pathogenesis at least in some situations although the drug is effective in vitro. Hence, we should carefully examine a possibility of dasatinib repositioning for EBV+ B cell malignancies.