bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrated TORC1 and PKA signaling control the temporal activation of glucose-induced gene expression in yeast
Authors: Kunkel Joseph , Luo Xiangxia , Capaldi Andrew P. 
Published: August 2019

AbstractThe growth rate of a yeast cell is controlled by the target of rapamycin kinase complex I (TORC1) and cAMP-dependent protein kinase (PKA) pathways. To determine how TORC1 and PKA cooperate to regulate cell growth, we performed temporal analysis of gene expression in yeast switched from a non-fermentable substrate, to glucose, in the presence and absence of TORC1 and PKA inhibitors. Quantitative analysis of these data reveals that PKA drives the expression of key cell growth genes during transitions into, and out of, the rapid growth state in glucose, while TORC1 is important for the steady-state expression of the same genes. This circuit design may enable yeast to set an exact growth rate based on the abundance of internal metabolites such as amino acids, via TORC1, but also adapt rapidly to changes in external nutrients, such as glucose, via PKA.
Recent advances and applications of machine learning in solid-state materials science
Authors: Schmidt Jonathan , Marques Mário R. G. , Botti Silvana , Marques Miguel A. L. 
Published: August 2019

AbstractOne of the most exciting tools that have entered the material science toolbox in recent years is machine learning. This collection of statistical methods has already proved to be capable of considerably speeding up both fundamental and applied research. At present, we are witnessing an explosion of works that develop and apply machine learning to solid-state systems. We provide a comprehensive overview and analysis of the most recent research in this topic. As a starting point, we introduce machine learning principles, algorithms, descriptors, and databases in materials science. We continue with the description of different machine learning approaches for the discovery of stable materials and the prediction of their crystal structure. Then we discuss research in numerous quantitative structure–property relationships and various approaches for the replacement of first-principle methods by machine learning. We review how active learning and surrogate-based optimization can be applied to improve the rational design process and related examples of applications. Two major questions are always the interpretability of and the physical understanding gained from machine learning models. We consider therefore the different facets of interpretability and their importance in materials science. Finally, we propose solutions and future research paths for various challenges in computational materials science.
Volcano-tectonic deformation in the Monti Sabatini Volcanic District at the gates of Rome (central Italy): evidence from new geochronologic constraints on the Tiber River MIS 5 terraces
Authors: Marra F. , Florindo F. , Jicha B. R. , Nomade S. , Palladino D. M. , Pereira A. , Sottili G. , Tolomei C. 
Published: August 2019

AbstractThe accumulation of magma within the Monti Sabatini Volcanic District (MSVD), Italy, coupled with the extensional tectonics of the region, pose both volcanic and tectonic hazards to the city of Rome, located 20 km to the southeast. We combine 40Ar/39Ar geochronology of volcanic deposits and a geomorphologic/stratigraphic/paleomagnetic study of fluvial terraces to determine the recurrence interval and the time elapsed since the last eruption of the MSVD. Moreover, we provide a date for the youngest known eruption of the MSVD and assess the timing of the most recent volcanic phase. Results of this study show: (i) The most recent eruptive phase occurred between 100 ka and 70 ka; (ii) the anomalously high elevation of the MIS 5 terrace indicates that it was concurrent with 50 m of uplift in the volcanic area; (iii) the time since the last eruption (70 ka) exceeds the average recurrence interval (39 ky) in the last 300 ky, as well as the longest previous dormancy (50 ky) in that time span. (iv) the current duration of dormancy is similar to the timespan separating the major explosive phase that occurred 590–450 ka.
Mechanically-induced GDF15 Secretion by Periodontal Ligament Fibroblasts Regulates Osteogenic Transcription
Authors: Symmank Judit , Zimmermann Sarah , Goldschmitt Jutta , Schiegnitz Eik , Wolf Michael , Wehrbein Heinrich , Jacobs Collin 
Published: August 2019

AbstractThe alveolar bone provides structural support against compressive and tensile forces generated during mastication as well as during orthodontic treatment. To avoid abnormal alveolar bone resorption and tooth loss, a balanced bone turnover by bone-degrading osteoclasts and bone-generating osteoblasts is of great relevance. Unlike its contradictory role in regulating osteoclast and osteoblast cell differentiation, the TGF-β/BMP-family member GDF15 is well known for its important functions in the regulation of cell metabolism, as well as cell fate and survival in response to cellular stress. Here, we provide first evidence for a potential role of GDF15 in translating mechanical stimuli into cellular changes in immature osteoblasts. We detected enhanced levels of GDF15 in vivo in periodontal ligament cells after the simulation of tooth movement in rat model system as well as in vitro in mechanically stressed human periodontal ligament fibroblasts. Moreover, mechanical stimulation enhanced GDF15 secretion by periodontal ligament cells and the stimulation of human primary osteoblast with GDF15 in vitro resulted in an increased transcription of osteogenic marker genes like RUNX2, osteocalcin (OCN) and alkaline phosphatase (ALP). Together, the present data emphasize for the first time a potential function of GDF15 in regulating differentiation programs of immature osteoblasts according to mechanical stimulation.
Water oxidation by Ferritin: A semi-natural electrode
Authors: Abdi Zahra , Bagheri Robabeh , Song Zhenlun , Najafpour Mohammad Mahdi 
Published: August 2019

AbstractFerritin is a protein (ca. 12 nm) with a central pocket of 6 nm diameter, and hydrated iron oxide stored in this central cavity of this protein. The protein shell has a complicated structure with 24 subunits. Transmission electron microscopy images of ferritin showed nanosized iron oxides (ca. 4–6 nm) in the protein structure. In high-resolution transmission electron microscopy images of the iron core, d-spacings of 2.5–2.6 Å were observed, which is corresponded to d-spacings of ferrihydrite crystal structure. Our experiments showed that at pH 11, the modified electrode by this biomolecule is active for water oxidation (turnover frequency: 0.001 s−1 at 1.7 V). Using affected by bacteria, we showed that Fe ions in the structure of ferritin are critical for water oxidation.
Nanoencapsulated betulinic acid analogue distinctively improves colorectal carcinoma in vitro and in vivo
Authors: Dutta Debasmita , Paul Brahamacharry , Mukherjee Biswajit , Mondal Laboni , Sen Suparna , Chowdhury Chinmay , Debnath Mita Chatterjee 
Published: August 2019

AbstractBetulinic acid, a plant secondary metabolite, has gained significant attention due to its antiproliferative activity over a range of cancer cells. A promising betulinic acid analogue (2c) with better therapeutic efficacy than parent molecule to colon carcinoma cells has been reported. Despite impressive biological applications, low aqueous solubility and bioavailability create difficulties for its therapeutic applications. To overcome these lacunae and make it as a promising drug candidate we have encapsulated the lead betulinic acid derivative (2c) in a polymeric nanocarrier system (2c-NP) and evaluated its in vitro and in vivo therapeutic efficacy. Apoptosis that induces in vitro antiproliferative activity was significantly increased by 2c-NP compared to free-drug (2c), as assured by MTT assay, Annexin V positivity, JC1 analysis and cell cycle study. The therapeutic potential measured in vitro and in vivo reflects ability of 2c-NP as an effective therapeutic agent for treatment of colon carcinoma and future translation to clinical trials.
Exosome surface glycans reflect osteogenic differentiation of mesenchymal stem cells: Profiling by an evanescent field fluorescence-assisted lectin array system
Authors: Shimoda Asako , Sawada Shin-ichi , Sasaki Yoshihiro , Akiyoshi Kazunari 
Published: August 2019

AbstractExtracellular vesicles (EVs) carry information between cells in the form of biomolecules. Such molecules have been found to serve as biomarkers. Glycans attached to surface molecules on EVs are involved in their cellular uptake. In this study, we examined glycan profiles of small EVs which are generally termed exosomes before and after osteogenic differentiation of adipose-derived mesenchymal stem cells (MSCs) by an evanescent field fluorescence-assisted (EFF)-lectin array system to discover glycan biomarkers for osteogenic differentiation. We found few differences between exosomes before and after osteogenic differentiation of MSCs in terms of fundamental characteristics such as size, morphology, and exosomal marker proteins. However, specific lectins bound strongly to exosomes from differentiated cells. Exosomes from osteogenically differentiated MSCs bound strongly to fucose- and mannose-binding lectins, especially at a high concentration of exosomes. In summary, we found that several lectins bound to exosomes from differentiated MSCs more strongly than to those from undifferentiated cells using an EFF-lectin array system, indicating that monitoring exosomal surface glycans may identify predictive indexes of osteogenic differentiation.
Restoring the Taxol biosynthetic machinery of Aspergillus terreus by Podocarpus gracilior Pilger microbiome, with retrieving the ribosome biogenesis proteins of WD40 superfamily
Authors: El-Sayed Ashraf S. A. , Mohamed Nabil Z. , Safan Samia , Yassin Marwa A. , Shaban Lamis , Shindia Ahmed A. , Shad Ali Gul , Sitohy Mahmoud Z. 
Published: August 2019

AbstractAttenuating the Taxol yield of Aspergillus terreus with the subculturing and storage were the technical challenges that prevent this fungus to be a novel platform for industrial Taxol production. Thus, the objective of this study was to unravel the metabolic machineries of A. terreus associated with attenuation of Taxol productivity, and their restoring potency upon cocultivation with the Podocarpus gracilior microbiome. The Taxol yield of A. terreus was drastically reduced with the fungal subculturing. At the 10th subculture, the yield of Taxol was reduced by four folds (78.2 µg/l) comparing to the original culture (268 µg/l), as authenticated from silencing of molecular expression of the Taxol-rate limiting enzymes (GGPPS, TDS, DBAT and BAPT) by qPCR analyses. The visual fading of A. terreus conidial pigmentation with the subculturing, revealing the biosynthetic correlation of melanin and Taxol. The level of intracellular acetyl-CoA influx was reduced sequentially with the fungal subculturing, rationalizing the decreasing on Taxol and melanin yields. Fascinatingly, the Taxol biosynthetic machinery and cellular acetyl-CoA of A. terreus have been completely restored upon addition of 3% surface sterilized leaves of P. gracilior, suggesting the implantation of plant microbiome on re-triggering the molecular machinery of Taxol biosynthesis, their transcriptional factors, and/or increasing the influx of Acetyl-CoA. The expression of the proteins of 74.4, 68.2, 37.1 kDa were exponentially suppressed with A. terreus subculturing, and strongly restored upon addition of P. gracilior leaves, ensuring their profoundly correlation with the molecular expression of Taxol biosynthetic genes. From the proteomic analysis, the restored proteins 74.4 kDa of A. terreus upon addition of P. gracilior leaves were annotated as ribosome biogenesis proteins YTM and microtubule-assembly proteins that belong to WD40 superfamily. Thus, further ongoing studies for molecular cloning and expression of these genes with strong promotors in A. terreus, have been initiated, to construct a novel platform of metabolically stable A. terreus for sustainable Taxol production. Attenuating the Taxol yield of A. terreus with the multiple-culturing and storage might be due to the reduction on main influx of acetyl-CoA, or downregulation of ribosome biogenesis proteins that belong to WD40 protein superfamily.
Investigation and Assessment for an effective approach to the reclamation of Polycyclic Aromatic Hydrocarbon (PAHs) contaminated site: SIN Bagnoli, Italy
Authors: Guarino Carmine , Zuzolo Daniela , Marziano Mario , Conte Barbara , Baiamonte Giuseppe , Morra Lorenzo , Benotti Daniele , Gresia Davide , Stacul Edoardo Robortella , Cicchella Domenico , Sciarrillo Rosaria 
Published: August 2019

AbstractNative plant species were screened for their remediation potential for the removal of Polycyclic Aromatic Hydrocarbons (PAHs) contaminated soil of Bagnoli brownfield site (Southern Italy). Soils at this site contain all of the PAHs congeners at concentration levels well above the contamination threshold limits established by Italian environmental legislation for residential/recreational land use, which represent the remediation target. The concentration of 13 High Molecular Weight Polycyclic Aromatic Hydrocarbons in soil rhizosphere, plants roots and plants leaves was assessed in order to evaluate native plants suitability for a gentle remediation of the study area. Analysis of soil microorganisms are provides important knowledge about bioremediation approach. Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria are the main phyla of bacteria observed in polluted soil. Functional metagenomics showed changes in dioxygenases, laccase, protocatechuate, and benzoate-degrading enzyme genes. Indolacetic acid production, siderophores release, exopolysaccharides production and ammonia production are the key for the selection of the rhizosphere bacterial population. Our data demonstrated that the natural plant-bacteria partnership is the best strategy for the remediation of a PAHs-contaminated soil.
Aspirin use is associated with reduced risk for recurrence of pyogenic liver abscess: a propensity score analysis
Authors: Liu Jia-Sin , Lee Chen-Hsiang , Chuah Seng-Kee , Tai Wei-Chen , Chang Chia-Chi , Chen Fang-Ju 
Published: August 2019

AbstractAspirin possesses anti-bacterial activity that may prevent recurrence ofKlebsiella pneumoniaepyogenic liver abscess (KP-PLA). In ex-vivostudy, aspirin was administered before bactericidal assay against serotype K1K. pneumoniae. We identified 5,912 patients with PLA who had no known pre-existing hepatobiliary diseases or malignancy in Taiwan from 1999 to 2013 from nationwide cohort study. Multivariate Cox proportional hazards regression models was used to estimate the hazard ratios [HR] for the association between aspirin use and recurrent PLA. The PLA recurrence rate in patients taking aspirin daily for 30 or more days, from 90 days before to 90 days after the first PLA episode (aspirin users), and aspirin non-users was 42.5 and 74.6 per 1,000 person-years of follow-up, respectively. The population-based study showed a HR for PLA recurrence in aspirin users of 0.50 (95% confidence interval, 0.35–0.69), relative to that in non-users, after adjustments for confounders. Anex-vivostudy indicated that aspirin was able to significantly enhance bacterial killing by leukocytes, whether collected from diabetic patients with KP-PLA recurrence or from healthy volunteers. Our results suggest that aspirin is associated with reduced risk for PLA recurrence among Taiwanese with PLA who had no preexisting hepatobiliary diseases or malignancy.
Dual-Energy X-Ray Absorptiometry Compared to Computed Tomography for Visceral Adiposity Assessment Among Gastrointestinal and Pancreatic Cancer Survivors
Authors: Coletta Adriana M. , Klopp Ann H. , Fogelman David , Parikh Aaroh M. , Li Yisheng , Garg Naveen , Basen-Engquist Karen 
Published: August 2019

AbstractDual-energy x-ray absorptiometry (DXA) for visceral adipose tissue (VAT) assessment is used as an alternative to computed tomography (CT) for research purposes in apparently healthy and clinical populations. It is unknown whether DXA is comparable to CT among cancer survivors, especially in cases where VAT assessment may be affected by treatment history and side effects and become more challenging to assess, such as a history of surgical gastrointestinal resection and/or ascites. The purpose of this study was to determine the level of agreement between DXA and CT when assessing VAT area and volume among cancer survivors. One hundred Gastrointestinal and pancreatic cancer survivors underwent abdominal and pelvis CT and whole-body DXA within 48 hours. Bland-Altman analysis revealed that in women and men, DXA VAT-area estimates were larger and smaller, respectively, and was consistently smaller in estimates for VAT-volume. Correlations from linear regression analysis revealed statistically significant positive correlations between measurement methods. Overall, while DXA VAT estimates are highly correlated with CT VAT estimates, DXA estimates show substantial bias which indicates the two methods are not interchangeable in this population. Further research is warranted with a larger, more homogeneous sample to develop better estimates of the bias.
Antibiotic use during pregnancy and childhood overweight: A population-based nationwide cohort study
Authors: Jess Tine , Morgen Camilla S. , Harpsøe Maria C. , Sørensen Thorkild I. A. , Ajslev Teresa A. , Antvorskov Julie C. , Allin Kristine H. 
Published: August 2019

AbstractStudies in mice suggest that early life represents a critical time window, where antibiotics may exert profound and lasting effects on the gut microbiota and metabolism. We aimed to test the hypothesis that prenatal antibiotic exposure is associated with increased risk of childhood overweight in a population-based cohort study. We linked 43,365 mother-child dyads from a nationwide cohort of pregnant women and their offspring to the Danish National Prescription Registry. Linear and logistic regression models were used to examine associations between prenatal exposure to antibiotics and BMI z-score and overweight (including obesity) at age seven and 11 years. Prenatal antibiotic exposure and childhood overweight were both associated with high pre-pregnancy BMI, maternal diabetes, multi-parity, smoking, low socioeconomic status, high paternal BMI, and short duration of breastfeeding. After adjustment for confounders, no associations were observed between prenatal antibiotic exposure and odds of overweight at age seven and 11 years. Whereas no association was observed between broad-spectrum antibiotics and overweight at age 11 years, exposure to broad-spectrum antibiotics was associated with higher odds of overweight at age seven years with an odds ratio of 1.27 (95% CI, 1.05–1.53) for ampicillin and an odds ratio of 1.56 (95% CI, 1.23–1.97) for amoxicillin. As we did not account for underlying infections, the observed associations with early childhood overweight could be explained by confounding by indication. In conclusion, our population-based study suggests that prenatal exposure to narrow-spectrum antibiotics is not associated with overweight in offspring. Exposure to some broad-spectrum antibiotics may increase the odds of overweight in early childhood, but the association does not persist in later childhood.
Green fabrication of stable lead-free bismuth based perovskite solar cells using a non-toxic solvent
Authors: Jain Sagar M. , Edvinsson Tomas , Durrant James R. 
Published: August 2019

AbstractThe very fast evolution in certified efficiency of lead-halide organic-inorganic perovskite solar cells to 24.2%, on par and even surpassing the record for polycrystalline silicon solar cells (22.3%), bears the promise of a new era in photovoltaics and revitalisation of thin film solar cell technologies. However, the presence of toxic lead and particularly toxic solvents during the fabrication process makes large-scale manufacturing of perovskite solar cells challenging due to legislation and environment issues. For lead-free alternatives, non-toxic tin, antimony and bismuth based solar cells still rely on up-scalable fabrication processes that employ toxic solvents. Here we employ non-toxic methyl-acetate solution processed (CH3NH3)3Bi2I9 films to fabricate lead-free, bismuth based (CH3NH3)3Bi2I9 perovskites on mesoporous TiO2 architecture using a sustainable route. Optoelectronic characterization, X-ray diffraction and electron microscopy show that the route can provide homogeneous and good quality (CH3NH3)3Bi2I9 films. Fine-tuning the perovskite/hole transport layer interface by the use of conventional 2,2′,7,7′-tetrakis (N,N′-di-p-methoxyphenylamino)−9,9′-spirbiuorene, known as Spiro-OMeTAD, and poly(3-hexylthiophene-2,5-diyl - P3HT as hole transporting materials, yields power conversion efficiencies of 1.12% and 1.62% under 1 sun illumination. Devices prepared using poly(3-hexylthiophene-2,5-diyl hole transport layer shown 300 h of stability under continuous 1 sun illumination, without the use of an ultra violet-filter.
Dose-adjusted and dose/kg-adjusted concentrations of mycophenolic acid precursors reflect metabolic ratios of their metabolites in contrast with tacrolimus and cyclosporine
Authors: Hryniewiecka Ewa , Żegarska Jolanta , Żochowska Dorota , Samborowska Emilia , Jaźwiec Radosław , Kosieradzki Maciej , Nazarewski Sławomir , Dadlez Michał , Pączek Leszek 
Published: August 2019

Abstract
Background and purpose: Therapeutic drug monitoring is a valuable tool supporting immunosuppressive therapy. Significant variation of immunosuppressive drug (ISD) concentrations during their use at similar doses is the basis of dose-normalization strategy. The strategy of dose-adjustment is proposed to identify variability in the rate of ISD metabolism. While the parent drug-to-metabolite ratio (metabolic ratio, MR) represents the rate of formation of individual metabolites. The present study was aimed at evaluation of associations between ISDs’ metabolism rate expressed as dose-adjusted concentrations (C/D) and dose/kg-adjusted concentrations (C/D/kg) and MRs of individual metabolites of tacrolimus, cyclosporine A and MPA precursors.
Experimental approach: 506 patients have participated: 284 males (56.13%) and 222 females (43.87%); 318 after kidney (62.85%) and 188 after liver transplantation; median age was 51.34 (39.32-59.95) years and median time after transplantation 78.92 (33.87-138.4) months.
Key results: Generally, we have not observed significant relationships between dose-adjusted and dose/kg-adjusted concentrations and MRs of cyclosporine and tacrolimus. Significant correlations were found for: AM9/CsA and dMC-CsA/CsA in kidney transplant recipients and MIII/Tac, AM1/CsA and AM4N/CsA in liver transplant recipients. In contrast, MRs of mycophenolic acid (MPA) metabolites correlated significantly with MPA C/D and C/D/kg both in kidney and liver transplant recipients.
Conclusion and implications: In conclusion, easily available and easy to use in clinical practice C/D and C/D/kg ratios cannot be considered as parameters directly reflecting the rate of generation of major metabolites of cyclosporine and tacrolimus both in liver and kidney transplant recipients.