bluuebunny/crossref_metadata_2025_split huggingface dataset:
De novo transcriptome assembly and analysis of the freshwater araphid diatom Fragilaria radians, Lake Baikal
Authors: Galachyants Yuri Pavlovich , Zakharova Yulia Robertovna , Volokitina Nadezda Antonovna , Morozov Alexey Anatolyevich , Likhoshway Yelena Valentinovna , Grachev Mikhail Aleksandrovich 
Published: September 2019

AbstractDiatoms are a group of eukaryotic microalgae populating almost all aquatic and wet environments. Their abundance and species diversity make these organisms significant contributors to biogeochemical cycles and important components of aquatic ecosystems. Although significant progress has been made in studies of Diatoms (Bacillariophyta) over the last two decades, since the spread of “omics” technologies, our current knowledge of the molecular processes and gene regulatory networks that facilitate environmental adaptation remain incomplete. Here, we present a transcriptome analysis ofFragilaria radiansisolated from Lake Baikal. The resulting assembly contains 27,446 transcripts encoding 21,996 putative proteins. The transcriptome assembly and annotation were coupled with quantitative experiments to search for differentially expressed transcripts between (i) exponential growth phase and dark-acclimated cell cultures, and (ii) those changing expression level during the early response to light treatment in dark-acclimated cells. The availability ofF.radiansgenome and transcriptome data provides the basis for future targeted studies of this species. Furthermore, our results extend taxonomic and environmental sampling of Bacillariophyta, opening new opportunities for comparative omics-driven surveys.
C/EBPδ protects from radiation-induced intestinal injury and sepsis by suppression of inflammatory and nitrosative stress
Authors: Banerjee Sudip , Fu Qiang , Shah Sumit K. , Melnyk Stepan B , Sterneck Esta , Hauer-Jensen Martin , Pawar Snehalata A. 
Published: September 2019

AbstractIonizing radiation (IR)-induced intestinal damage is characterized by a loss of intestinal crypt cells, intestinal barrier disruption and translocation of intestinal microflora resulting in sepsis-mediated lethality. We have shown that mice lacking C/EBPδ display IR-induced intestinal and hematopoietic injury and lethality. The purpose of this study was to investigate whether increased IR-induced inflammatory, oxidative and nitrosative stress promote intestinal injury and sepsis-mediated lethality in Cebpd−/− mice. We found that irradiated Cebpd−/− mice show decreased villous height, crypt depth, crypt to villi ratio and expression of the proliferation marker, proliferating cell nuclear antigen, indicative of intestinal injury. Cebpd−/− mice show increased expression of the pro-inflammatory cytokines (Il-6, Tnf-α) and chemokines (Cxcl1, Mcp-1, Mif-1α) and Nos2 in the intestinal tissues compared to Cebpd+/+ mice after exposure to TBI. Cebpd−/− mice show decreased GSH/GSSG ratio, increased S-nitrosoglutathione and 3-nitrotyrosine in the intestine indicative of basal oxidative and nitrosative stress, which was exacerbated by IR. Irradiated Cebpd-deficient mice showed upregulation of Claudin-2 that correlated with increased intestinal permeability, presence of plasma endotoxin and bacterial translocation to the liver. Overall these results uncover a novel role for C/EBPδ in protection against IR-induced intestinal injury by suppressing inflammation and nitrosative stress and underlying sepsis-induced lethality.
Real-time characterization of spectral instabilities in a mode-locked fibre laser exhibiting soliton-similariton dynamics
Authors: Lapre Coraline , Billet Cyril , Meng Fanchao , Ryczkowski Piotr , Sylvestre Thibaut , Finot Christophe , Genty Göery , Dudley John M. 
Published: September 2019

AbstractThe study of dissipative solitons in mode-locked lasers reveals a rich landscape of interaction dynamics resulting from the interplay of nonlinearity, dispersion and dissipation. Here, we characterize a range of instabilities in a dissipative soliton fibre laser in a regime where both conventional soliton and similariton propagation play significant roles in the intracavity pulse shaping. Specifically, we use the Dispersive Fourier Transform technique to perform real-time spectral measurements of buildup dynamics from noise to the generation of stable single pulses, phase evolution dynamics of bound state “similariton molecules”, and several examples of intermittent instability and explosion dynamics. These results show that the instabilities previously seen in other classes of passively mode-locked fibre lasers are also observed in the presence of strong nonlinear attraction of similariton evolution in an optical fibre amplifier.
Quantitative proteomic analysis of enhanced cellular effects of electrochemotherapy with Cisplatin in triple-negative breast cancer cells
Authors: Mittal Lakshya , Aryal Uma K. , Camarillo Ignacio G. , Ferreira Rodrigo M. , Sundararajan Raji 
Published: September 2019

AbstractDue to the lack of the three main receptors, triple negative breast cancer (TNBC) is refractive to standard chemotherapy. Hence, alternate therapies are needed. TNBCs utilize glycolysis, which heightens their growth, proliferation, invasiveness, chemotherapeutic resistance and poor therapeutic response. This calls for novel therapeutic strategies to target these metabolic vulnerabilities present in TNBC. Electroporation-mediated chemotherapy, known as electrochemotherapy (ECT) is gaining momentum as an attractive alternative. However, its molecular mechanisms need better understanding. Towards this, label-free quantitative proteomics is utilized to gain insight into the anticancer mechanisms of ECT using electrical pulses (EP) and Cisplatin (CsP) on MDA-MB-231, human TNBC cells. The results indicate that EP + CsP significantly downregulated 14 key glycolysis proteins (including ENO1, LDHA, LDHB, ACSS2, ALDOA, and PGK1), compared to CsP alone. EP + CsP caused a switch in the metabolism with upregulation of 34 oxidative phosphorylation pathway proteins and 18 tricarboxylic acid (TCA) cycle proteins compared to CsP alone, accompanied by the upregulation of proteins linked to several metabolic reactions, which produce TCA cycle intermediates. Moreover, EP + CsP promoted multiple pathways to cause 1.3-fold increase in the reactive oxygen species concentration and induced apoptosis. The proteomics results correlate well with cell viability, western blot, and qPCR data. While some effects were similar for EP, more comprehensive and long-lasting effects were observed for EP + CsP, which demonstrate the potential of EP + CsP against TNBC cells.
Study of Abnormal Group Velocities in Flexural Metamaterials
Authors: Park Hong Woo , Oh Joo Hwan 
Published: September 2019

AbstractGenerally, it has been known that the optical branch of a simple one-dimensional periodic structure has a negative group velocity at the first Brillouin zone due to the band-folding effect. However, the optical branch of the flexural wave in one-dimensional periodic structure doesn’t always have negative group velocity. The problem is that the condition whether the group velocity of the flexural optical branch is negative, positive or positive-negative has not been studied yet. In consequence, who try to achieve negative group velocity has suffered from trial-error process without an analytic guideline. In this paper, the analytic investigation for this abnormal behavior is carried out. In particular, we discovered that the group velocity of the optical branch in flexural metamaterials is determined by a simple condition expressed in terms of a stiffness ratio and inertia ratio of the metamaterial. To derive the analytic condition, an extended mass-spring system is used to calculate the wave dispersion relationship in flexural metamaterials. For the validation, various numerical simulations are carried out, including a dispersion curve calculation and three-dimensional wave simulation. The results studied in this paper are expected to provide new guidelines in designing flexural metamaterials to have desired wave dispersion curves.
Heterotrophy as a tool to overcome the long and costly autotrophic scale-up process for large scale production of microalgae
Authors: Barros A. , Pereira H. , Campos J. , Marques A. , Varela J. , Silva J. 
Published: September 2019

AbstractIndustrial scale-up of microalgal cultures is often a protracted step prone to culture collapse and the occurrence of unwanted contaminants. To solve this problem, a two-stage scale-up process was developed – heterotrophically Chlorella vulgaris cells grown in fermenters (1st stage) were used to directly inoculate an outdoor industrial autotrophic microalgal production unit (2nd stage). A preliminary pilot-scale trial revealed that C. vulgaris cells grown heterotrophically adapted readily to outdoor autotrophic growth conditions (1-m3 photobioreactors) without any measurable difference as compared to conventional autotrophic inocula. Biomass concentration of 174.5 g L−1, the highest value ever reported for this microalga, was achieved in a 5-L fermenter during scale-up using the heterotrophic route. Inocula grown in 0.2- and 5-m3 industrial fermenters with mean productivity of 27.54 ± 5.07 and 31.86 ± 2.87 g L−1 d−1, respectively, were later used to seed several outdoor 100-m3 tubular photobioreactors. Overall, all photobioreactor cultures seeded from the heterotrophic route reached standard protein and chlorophyll contents of 52.18 ± 1.30% of DW and 23.98 ± 1.57 mg g−1 DW, respectively. In addition to providing reproducible, high-quality inocula, this two-stage approach led to a 5-fold and 12-fold decrease in scale-up time and occupancy area used for industrial scale-up, respectively.
Structural insight into glucose repression of the mannitol operon
Authors: Choe Mangyu , Min Huitae , Park Young-Ha , Kim Yeon-Ran , Woo Jae-Sung , Seok Yeong-Jae 
Published: September 2019

AbstractCarbon catabolite repression is a regulatory mechanism to ensure sequential utilization of carbohydrates and is usually accomplished by repression of genes for the transport and metabolism of less preferred carbon compounds by a more preferred one. Although glucose and mannitol share the general components, enzyme I and HPr, of the phosphoenolpyruvate-dependent phosphotransferase system (PTS) for their transport, glucose represses the transport and metabolism of mannitol in a manner dependent on the mannitol operon repressor MtlR in Escherichia coli. In a recent study, we identified the dephosphorylated form of HPr as a regulator determining the glucose preference over mannitol by interacting with and augmenting the repressor activity of MtlR in E. coli. Here, we determined the X-ray structure of the MtlR-HPr complex at 3.5 Å resolution to understand how phosphorylation of HPr impedes its interaction with MtlR. The phosphorylation site (His15) of HPr is located close to Glu108 and Glu140 of MtlR and phosphorylation at His15 causes electrostatic repulsion between the two proteins. Based on this structural insight and comparative sequence analyses, we suggest that the determination of the glucose preference over mannitol solely by the MtlR-HPr interaction is conserved within the Enterobacteriaceae family.
Arc-arc collision caused the 2018 Eastern Iburi earthquake (M 6.7) in Hokkaido, Japan
Authors: Hua Yuanyuan , Zhao Dapeng , Xu Yixian , Wang Zewei 
Published: September 2019

AbstractInland crustal earthquakes usually occur in the brittle upper crust (0–20 km depths), but the 6 September 2018 Eastern Iburi earthquake (M 6.7) took place in southern Hokkaido with a focal depth of ~37 km, causing 41 fatalities and serious damage to the local infrastructure. The reason why this event was so deep and its causal mechanism are still unclear. In this work we study the three-dimensional P and S wave seismic attenuation (1/Q) structure in the source zone of the 2018 Iburi earthquake. Our results show that this event occurred at the boundary between the Sorachi-Yezo belt (low Q) and the dipping Northeastern (NE) Japan arc (high Q) that is descending beneath the Kuril arc. The collision between the NE Japan and Kuril arcs as well as fluids from dehydration of the subducting Pacific plate caused this big event and its unusual focal depth. Similar attenuation structures are revealed in source zones of the 1970 Hidaka earthquake (M 6.7) and the 1982 Urakawa-oki earthquake (M 7.1), suggesting that they were caused by similar processes. We think that large earthquakes will take place again on the active thrust faults in southern Hokkaido in the coming decades. Hence, we should pay much attention to the seismic risk and prepare for reduction of earthquake hazards there.
Optimal management of oil content variability in olive mill batches by NIR spectroscopy
Authors: Correa E. C. , Roger J. M. , Lleó L. , Hernández-Sánchez N. , Barreiro P. , Diezma B. 
Published: September 2019

AbstractTotal oil content (OC) is one of the main parameters used to characterize the whole of olives entering a commercial mill, quantified by the total fresh weight of the lot and the oil concentration (%) assessed in a representative sample on olive paste, by means of chemical extraction. Nuclear magnetic resonance (NMR) and NIR spectroscopy are alternative methods even at individual olives. This work evaluates several strategies to calibrate precise NIR models for the estimation of the total OC. To this end, 278 olives were analysed covering whole season variability in terms of olive fresh-weight and the corresponding OC by chemical extraction in 31 batches. The average spectra from hyperspectral NIR images (1003–2208 nm) were computed for each fruit and the actual OC (g) of those olives determined by NMR (0.09 to 1.29 g with a precision of 0.017 g). According to the results, current batch based assessment of the OC (Soxhlet, %) in mills only reproduces 44% of the underlying heterogeneity, despite being the factory standard. The incorporation of individual NIR spectra (278) to the 31 Soxhlet values of the batches allows a 67% explanation of the OC (%) of olives. When estimating OC (g) gathering individual fresh weight and the estimation of oil concentration in olives, a standard error of prediction of 0.061 g is reached (r2 = 0.93), a precision value that approaches the potential limit according to the NMR reference (0.017 g).
A multi-source data integration approach reveals novel associations between metabolites and renal outcomes in the German Chronic Kidney Disease study
Authors: Altenbuchinger Michael , Zacharias Helena U. , Solbrig Stefan , Schäfer Andreas , Büyüközkan Mustafa , Schultheiß Ulla T. , Kotsis Fruzsina , Köttgen Anna , Spang Rainer , Oefner Peter J. , Krumsiek Jan , Gronwald Wolfram 
Published: September 2019

AbstractOmics data facilitate the gain of novel insights into the pathophysiology of diseases and, consequently, their diagnosis, treatment, and prevention. To this end, omics data are integrated with other data types, e.g., clinical, phenotypic, and demographic parameters of categorical or continuous nature. We exemplify this data integration issue for a chronic kidney disease (CKD) study, comprising complex clinical, demographic, and one-dimensional1H nuclear magnetic resonance metabolic variables. Routine analysis screens for associations of single metabolic features with clinical parameters while accounting for confounders typically chosen by expert knowledge. This knowledge can be incomplete or unavailable. We introduce a framework for data integration that intrinsically adjusts for confounding variables. We give its mathematical and algorithmic foundation, provide a state-of-the-art implementation, and evaluate its performance by sanity checks and predictive performance assessment on independent test data. Particularly, we show that discovered associations remain significant after variable adjustment based on expert knowledge. In contrast, we illustrate that associations discovered in routine univariate screening approaches can be biased by incorrect or incomplete expert knowledge. Our data integration approach reveals important associations between CKD comorbidities and metabolites, including novel associations of the plasma metabolite trimethylamine-N-oxide with cardiac arrhythmia and infarction in CKD stage 3 patients.
Dynamic secondary electron emission in rough composite materials
Authors: Olano Leandro , Dávila Maria E. , Dennison John R. , Martín-Iglesias Petronilo , Montero Isabel 
Published: September 2019

AbstractThe interaction of ionizing radiation with matter is of critical importance in numerous areas of science and technology like space and vacuum technology and even medicine and biotechnology. Secondary electron emission is a consequence of electron irradiation on materials. We achieve extremely low secondary electron emission yield values smaller than 0.2, even up to incident electron energies ~1 keV, due to an undocumented synergy between neighbouring metal and dielectric domains in composite samples. To investigate this experimental discovery, we propose a simple 3D model where the dielectric and metallic domains are arranged in parallel and interleaved. The proposed surface profile has a triangular shape to model the surface roughness. We obtain a continuous equation to describe the electric field that arises between grounded conductors and charged dielectrics domains. The calculated trajectories of secondary electrons in this 3D geometry are used to predict dynamic secondary emission yield, which strongly depends on the charge accumulated in the dielectric domains. This research paves the way to design new materials of low secondary emission yield, addressing the technological problem not yet resolved to inhibit the electron avalanche in RF equipment that limit their maximum working power.
Doping Strontium into Neodymium Manganites Nanocomposites for Enhanced Visible light Driven Photocatalysis
Authors: Abdel-Latif I. A. , Al-Hajji L. A. , Faisal M. , Ismail Adel A. 
Published: September 2019

AbstractNd1−xSrxMnO3 nanocomposites perovskites were synthesized using sol gel method at different Sr content x = 0.3, 0.5, 0.7, and 0.9. The photocatalytic performance of the Nd1−xSrxMnO3 nanocomposites for photodegradation of Acridine orange dye (AO) was evaluated over visible light illumination. The single phase of orthorhombic pbnm was formed for x = 0.3 and 0.5; however monoclinic and orthorhombic were observed at x = 0.7 and 0.9. The Energy gap of the Nd1−xSrxMnO3 nanocomposites were estimated for all concentrations to be in the range of 3 ± 0.05 eV. The photocatalytic efficiency of Nd0.3Sr0.7MnO3 nanocomposite was 95% of the initial AO dye concentration within 3 h illumination time. The linear increase of the photodegradation rate was found in our samples as a result of the increase of Sr contents from 0.3 to 0.7wt %. Interestingly, the Nd0.3Sr0.7MnO3 content has the highest degradation rate of AO which is two times faster than undoped NdMnO3. This superior behavior in photocatalytic activity of Nd0.3Sr0.7MnO3 nanocomposite emerges from large surface area, structural anisotropy, and small particle size. These findings shows convincingly that the Nd1−xSrxMnO3 photocatalysts possess great promise for visible light driven photodegradation of AO dye.
Increase in fatty acids and flotillins upon resveratrol treatment of human breast cancer cells
Authors: Gomes Luciana , Sorgine Marcos , Passos Carlos Luan Alves , Ferreira Christian , de Andrade Ivone Rosa , Silva Jerson L. , Atella Georgia C. , Mermelstein Claudia S. , Fialho Eliane 
Published: September 2019

AbstractFlotillin-1 and flotillin-2 are highly conserved proteins that localize into cholesterol-rich microdomains in cellular membranes. Flotillins are closely related to the occurrence and development of various types of human cancers. Flotillin-1 is highly expressed in breast cancer, and the high expression level of flotillin-1 is significantly correlated with poorer patient survival. Here we studied the relationship between the formation of lipid rafts and the expression of flotillins and lipids in human breast cancer cells. We used the polyphenol compound resveratrol to alter the structure and function of the plasma membrane. Our data revealed an increase in fatty acids in MCF-7 and MDA-MB-231 cells upon resveratrol treatment. Interestingly, we also found an increase in the expression of both flotillin-1 and flotillin-2 in breast tumor cells after treatment. Resveratrol also induced changes in the pattern of flotillin distribution among detergent-resistant lipid rafts fractions in both cell lines and induced the nuclear translocation of flotillin-2. Since resveratrol has been pointed out as a putative cancer therapy agent, our results could have an impact on the understanding of the effects of resveratrol in tumor cells.
Processing of a single ribonucleotide embedded into DNA by human nucleotide excision repair and DNA polymerase η
Authors: Sassa Akira , Tada Haruto , Takeishi Ayuna , Harada Kaho , Suzuki Megumi , Tsuda Masataka , Sasanuma Hiroyuki , Takeda Shunichi , Sugasawa Kaoru , Yasui Manabu , Honma Masamitsu , Ura Kiyoe 
Published: September 2019

AbstractDNA polymerases often incorporate non-canonical nucleotide, i.e., ribonucleoside triphosphates into the genomic DNA. Aberrant accumulation of ribonucleotides in the genome causes various cellular abnormalities. Here, we show the possible role of human nucleotide excision repair (NER) and DNA polymerase η (Pol η) in processing of a single ribonucleotide embedded into DNA. We found that the reconstituted NER system can excise the oxidized ribonucleotide on the plasmid DNA. Taken together with the evidence that Pol η accurately bypasses a ribonucleotide, i.e., riboguanosine (rG) or its oxidized derivative (8-oxo-rG) in vitro, we further assessed the mutagenic potential of the embedded ribonucleotide in human cells lacking NER or Pol η. A single rG on the supF reporter gene predominantly induced large deletion mutations. An embedded 8-oxo-rG caused base substitution mutations at the 3′-neighboring base rather than large deletions in wild-type cells. The disruption of XPA, an essential factor for NER, or Pol η leads to the increased mutant frequency of 8-oxo-rG. Furthermore, the frequency of 8-oxo-rG-mediated large deletions was increased by the loss of Pol η, but not XPA. Collectively, our results suggest that base oxidation of the embedded ribonucleotide enables processing of the ribonucleotide via alternative DNA repair and damage tolerance pathways.
Saving Old Bones: a non-destructive method for bone collagen prescreening
Authors: Sponheimer Matt , Ryder Christina M. , Fewlass Helen , Smith Erin K. , Pestle William J. , Talamo Sahra 
Published: September 2019

AbstractBone collagen is an important material for radiocarbon, paleodietary, and paleoproteomic analyses, but it degrades over time, making such analyses more difficult with older material. Collagen preservation between and within archaeological sites is also variable, so that much time, effort, and money can go into the preparation and initial analysis of samples that will not yield meaningful results. To avoid this, various methods are employed to prescreen bone for collagen preservation (e.g., %N, microporosity, and FTIR spectroscopic analyses), but these are often destructive and/or require exportation for analysis. Here, we explore near-infrared spectroscopy as a tool for gauging the collagen content of ground and whole bone from about 500 to 45,000 years ago. We show that a portable spectrometer’s ability to quantify collagen content and classify specimens by preservation status is comparable to that of other popular prescreening methods. Moreover, near-infrared spectroscopy is non-destructive and spectra can be acquired in a few seconds.