bluuebunny/crossref_metadata_2025_split huggingface dataset:
A cellular automaton model for spheroid response to radiation and hyperthermia treatments
Authors: Brüningk Sarah C. , Ziegenhein Peter , Rivens Ian , Oelfke Uwe , Haar Gail ter 
Published: November 2019

AbstractThermo-radiosensitisation is a promising approach for treatment of radio-resistant tumours such as those containing hypoxic subregions. Response prediction and treatment planning should account for tumour response heterogeneity, e.g. due to microenvironmental factors, and quantification of the biological effects induced. 3D tumour spheroids provide a physiological in vitro model of tumour response and a systems oncology framework for simulating spheroid response to radiation and hyperthermia is presented. Using a cellular automaton model, 3D oxygen diffusion, delivery of radiation and/or hyperthermia were simulated for many ($${\bf{1}}{{\bf{0}}}^{{\bf{4}}}{\boldsymbol{-}}{\bf{1}}{{\bf{0}}}^{{\bf{7}}}$$
1

0

4

−

1

0

7

) individual cells forming a spheroid. The iterative oxygen diffusion model was compared to an analytical oxygenation model and simulations were calibrated and validated against experimental data for irradiated (0–10 Gy) and/or heated (0–240 CEM43) HCT116 spheroids. Despite comparable clonogenic survival, spheroid growth differed significantly following radiation or hyperthermia. This dynamic response was described well by the simulation ($${{\bf{R}}}^{{\bf{2}}}$$

R

2

> 0.85). Heat-induced cell death was implemented as a fast, proliferation-independent process, allowing reoxygenation and repopulation, whereas radiation was modelled as proliferation-dependent mitotic catastrophe. This framework stands out both through its experimental validation and its novel ability to predict spheroid response to multimodality treatment. It provides a good description of response where biological dose-weighting based on clonogenic survival alone was insufficient.
High efficacy full allelic CRISPR/Cas9 gene editing in tetraploid potato
Authors: Johansen Ida Elisabeth , Liu Ying , Jørgensen Bodil , Bennett Eric Paul , Andreasson Erik , Nielsen Kåre L. , Blennow Andreas , Petersen Bent Larsen 
Published: November 2019

AbstractCRISPR/Cas9 editing efficacies in tetraploid potato were highly improved through the use of endogenous potato U6 promoters. Highly increased editing efficiencies in the Granular Bound Starch Synthase gene at the protoplast level were obtained by replacement of the Arabidopsis U6 promotor, driving expression of the CRISPR component, with endogenous potato U6 promotors. This translated at the ex-plant level into 35% full allelic gene editing. Indel Detection Amplicon Analysis was established as an efficient tool for fast assessment of gene editing in complex genomes, such as potato. Together, this warrants significant reduction of laborious cell culturing, ex-plant regeneration and screening procedures of plants with high complexity genomes.
The complete mitochondrial genome of Harpago chiragra and Lambis lambis (Gastropoda: Stromboidea): implications on the Littorinimorpha phylogeny
Authors: Jiang Dianhang , Zheng Xiaodong , Zeng Xiaoqi , Kong Lingfeng , Li Qi 
Published: November 2019

AbstractThe complete mitochondrial genomes ofHarpago chiragraandLambis lambis(Strombidae) were determined with the size of 15,460 bp and 15,481 bp, respectively, and both sequences contained 13 protein-coding genes, 22 tRNAs, and two rRNAs.H. chiragraandL. lambishave similar mitochondrial features, corresponding to typical gastropod mitochondrial genomes, such as the conserved gene order, a high A + T content (66.22% forH. chiragraand 66.10% forL. lambis), and preference for A + T-rich codons. The start or termination codon of same protein-coding gene inH. chiragrawas consistent with that inL. lambis, except for the termination codon ofcox1gene (TAG forH. chiragraand TAA forL. lambis) and the start codon ofnad4(GTG forH. chiragraand ATG forL. lambis). Pairwise sequence alignments detected different degrees of variations inH. chiragraandL. lambismitochondrial genomes; and the two species had lower levels of genetic distance (0.202 for nucleotide sequence) and closest relationships as compared toStrombus gigasandOncomelania hupensis. The 13 partitioned nucleotide sequences of protein coding genes ofH. chiragraandL. lambiswere aligned with representatives of the main lineages of gastropods and their phylogenetic relationships were inferred.H. chiragraandL. lambisshare the same gene order as Littorinimorpha species, except Vermetoidea, which demonstrate a gene rearrangement in species. The reconstructed phylogeny supports three major clades within Littorinimorpha: 1) Stromboidea, Tonnoidea, Littorinoidea, and Naticoidea, 2) Rissooidea and Truncatelloidea, and 3) Vermetoidea. In addition, a relaxed molecular clock calibrated with fossils dated the diversification of Strombidae near 112 (44–206) Mya and a possible radiation is detected to occur between 45–75 Mya, providing implications to understand the Cenozoic replacement event (65–135 Mya) of Aporrhaidae by Strombidae.
Compound Specific Carbon Isotope Analysis in Sake by LC/IRMS and Brewers’ Alcohol Proportion
Authors: Suto Momoka , Kawashima Hiroto 
Published: November 2019

AbstractSake is a traditional Japanese alcohol. Nowadays, the consumption for Sake is increasing in worldwide and its popularity is growing. However, there are act of fraudulence by additional brewers’ alcohol and sugar. Therefore, a method is needed to find illegal fraud on label. In this work, we analyzed the δ13C values of the ethanol (δ13Ceth) and glucose (δ13Cglu) in Sake by liquid chromatography combined with isotope ratio mass spectrometry for the first time. Further, we developed the criteria using δ13Ceth and δ13Cglu to check brewers’ alcohol and sugar. In addition, there are some sake categories (Ginjyo and Futsu-shu) allowed to additional brewers’ alcohol up to legally determined percentage. The experimental additions of brewers’ alcohol from a C4 plant were conducted to Junmai, as sake by C3 plants. There was a strong correlation (R = 0.98, P < 0.05) between the percentage of added brewers’ alcohol and the δ13C values. We developed the method using the relationship for calculating percentage of brewers’ alcohol for the first time and estimated the percentage for commercial sake. Further, the price of sake was found to be inversely related to the percentage of brewers’ alcohol in the sake.
Effect of Different Insulin Therapies on Obstetric-Fetal Outcomes
Authors: López-Tinoco Cristina , Jiménez-Blázquez José Luis , Larrán-Escandón Laura , Roca-Rodríguez María del Mar , Bugatto Fernando , Aguilar-Diosdado Manuel 
Published: November 2019

AbstractTo evaluate the effectiveness of the different insulin therapies on obstetrics-fetal outcomes in women with pregestational diabetes mellitus. We enrolled 147 pregnant women with pre-existing type 1 or 2 diabetes mellitus. Clinical and biochemical parameters were analysed in relation to obstetric and fetal outcomes. 14.2% received treatment with Neutral Protamine Hagedorn insulin and short-acting insulin analogues; 19% with premixed human insulin; 40.1% with insulin glargine and lispro, 6.2% with detemir and aspart and 20% with continuous subcutaneous insulin infusion. All 5 types of treatment achieved a reduction of the mean HbA1c during pregnancy (p = 0.01). Pre-pregnancy care was carried out for 48% of patients. We found no statistically significant differences between the different insulin therapies and the obstetric-fetal outcomes. In conclusión, the different insulin therapies used in patients with pregestational diabetes mellitus does not seem to affect obstetric-fetal outcomes.
Palindromic sequence-targeted (PST) PCR: a rapid and efficient method for high-throughput gene characterization and genome walking
Authors: Kalendar Ruslan , Shustov Alexandr V. , Seppänen Mervi M. , Schulman Alan H. , Stoddard Frederick L. 
Published: November 2019

AbstractGenome walking (GW) refers to the capture and sequencing of unknown regions in a long DNA molecule that are adjacent to a region with a known sequence. A novel PCR-based method, palindromic sequence-targeted PCR (PST-PCR), was developed. PST-PCR is based on a distinctive design of walking primers and special thermal cycling conditions. The walking primers (PST primers) match palindromic sequences (PST sites) that are randomly distributed in natural DNA. The PST primers have palindromic sequences at their 3′-ends. Upstream of the palindromes there is a degenerate sequence (8–12 nucleotides long); defined adapters are present at the 5′-termini. The thermal cycling profile has a linear amplification phase and an exponential amplification phase differing in annealing temperature. Changing the annealing temperature to switch the amplification phases at a defined cycle controls the balance between sensitivity and specificity. In contrast to traditional genome walking methods, PST-PCR is rapid (two to three hours to produce GW fragments) as it uses only one or two PCR rounds. Using PST-PCR, previously unknown regions (the promoter and intron 1) of the VRN1 gene of Timothy-grass (Phleum pratense L.) were captured for sequencing. In our experience, PST-PCR had higher throughput and greater convenience in comparison to other GW methods.
A diarylamine derived from anthranilic acid inhibits ZIKV replication
Authors: Silva Suely , Shimizu Jacqueline Farinha , Oliveira Débora Moraes de , Assis Leticia Ribeiro de , Bittar Cintia , Mottin Melina , Sousa Bruna Katiele de Paula , Mesquita Nathalya Cristina de Moraes Roso , Regasini Luis Octávio , Rahal Paula , Oliva Glaucius , Perryman Alexander Luke , Ekins Sean , Andrade Carolina Horta , Goulart Luiz Ricardo , Sabino-Silva Robinson , Merits Andres , Harris Mark , Jardim Ana Carolina Gomes 
Published: November 2019

AbstractZika virus (ZIKV) is a mosquito-transmitted Flavivirus, originally identified in Uganda in 1947 and recently associated with a large outbreak in South America. Despite extensive efforts there are currently no approved antiviral compounds for treatment of ZIKV infection. Here we describe the antiviral activity of diarylamines derived from anthranilic acid (FAMs) against ZIKV. A synthetic FAM (E3) demonstrated anti-ZIKV potential by reducing viral replication up to 86%. We analyzed the possible mechanisms of action of FAM E3 by evaluating the intercalation of this compound into the viral dsRNA and its interaction with the RNA polymerase of bacteriophage SP6. However, FAM E3 did not act by these mechanisms.In silicoresults predicted that FAM E3 might bind to the ZIKV NS3 helicase suggesting that this protein could be one possible target of this compound. To test this, the thermal stability and the ATPase activity of the ZIKV NS3 helicase domain (NS3Hel) were investigatedin vitroand we demonstrated that FAM E3 could indeed bind to and stabilize NS3Hel.
Zn2+ stimulates salivary secretions via metabotropic zinc receptor ZnR/GPR39 in human salivary gland cells
Authors: Kim Yoon-Jung , Jo Youhwa , Lee Yeon-Hee , Park Kyungpyo , Park Hee-Kyung , Choi Se-Young 
Published: November 2019

AbstractZn2+ is a divalent cation that is essential for many biological activities, as it influences many ion channels and enzymatic activities. Zn2+ can evoke G-protein-coupled receptor signaling via activation of the metabotropic zinc receptor ZnR/GPR39. In spite of evidence suggesting the presence of ZnR/GPR39 in salivary gland cells, there has been no evidence of ZnR/GPR39-mediated modulation of salivary gland function. Here we characterized the role of ZnR/GPR39 in human submandibular gland cells. A 0.25% ZnCl2 solution evoked secretion of unstimulated and stimulated whole saliva in humans. We found that ZnR/GPR39 is expressed in human submandibular glands and HSG cells. Zn2+ increased cytosolic Ca2+ concentration ([Ca2+]i) in a concentration-dependent manner. Muscarinic antagonist had no effect on Zn2+-induced [Ca2+]i increase, which was completely blocked by the phospholipase C-β inhibitor. As with muscarinic agonist, Zn2+ also induced the translocation of aquaporin-5 (AQP-5) to the plasma membrane, which was drastically decreased in ZnR/GPR39-knockdown cells. These data suggest that the metabotropic Zn2+ receptor ZnR/GPR39 can modulate salivary secretion in human submandibular gland cells independent of muscarinic or histamine receptor signaling.
Physics-informed Deep Learning for Dual-Energy Computed Tomography Image Processing
Authors: Poirot Maarten G. , Bergmans Rick H. J. , Thomson Bart R. , Jolink Florine C. , Moum Sarah J. , Gonzalez Ramon G. , Lev Michael H. , Tan Can Ozan , Gupta Rajiv 
Published: November 2019

AbstractDual-energy CT (DECT) was introduced to address the inability of conventional single-energy computed tomography (SECT) to distinguish materials with similar absorbances but different elemental compositions. However, material decomposition algorithms based purely on the physics of the underlying attenuation process have several limitations, leading to low signal-to-noise ratio (SNR) in the derived material-specific images. To overcome these, we trained a convolutional neural network (CNN) to develop a framework to reconstruct non-contrast SECT images from DECT scans. We show that the traditional physics-based decomposition algorithms do not bring to bear the full information content of the image data. A CNN that leverages the underlying physics of the DECT image generation process as well as the anatomic information gleaned via training with actual images can generate higher fidelity processed DECT images.
Sema4C mediates EMT inducing chemotherapeutic resistance of miR-31-3p in cervical cancer cells
Authors: Jing Li , Bo Wang , Yourong Feng , Tian Wang , Shixuan Wang , Mingfu Wu 
Published: November 2019

AbstractSema4C, the target of many miRNAs, is involved in EMT-mediated chemotherapeutic resistance of many malignant tumors. However, the underlying upstream regulatory mechanisms of Sema4C-induced EMT and Sema4C-mediated drug resistance are still unclear. The aim of this study was to explore the potential role of miR-31-3p/Sema4C in regulating EMT in cisplatin-resistant (CR) cervical cancer cells. High expression levels of Sema4C were more frequently found in cervical cancer tissues and were associated with poor prognosis, whereas miR-31-3p was significantly downregulated in cervical cancer tissues, which was associated with shorter disease-free and overall survival. Overexpression of miR-31-3p inhibited malignant behaviors and EMT of cervical cancer cells in vitro. Furthermore, miR-31-3p was identified to directly target Sema4C, and upregulation of miR-31-3p reversed EMT-mediated biological functions, including cisplatin resistance of Sema4C in cervical cancer cells. These results suggest that Sema4C promoted EMT-mediated cisplatin resistance in cervical cancer cells and that this effect was inhibited by overexpression of miR-31-3p. Thus, silencing Sema4C or overexpression of miR-31-3p could be a novel approach to treat drug resistance to chemotherapy in cervical cancers.
A new source of root-knot nematode resistance from Arachis stenosperma incorporated into allotetraploid peanut (Arachis hypogaea)
Authors: Ballén-Taborda Carolina , Chu Ye , Ozias-Akins Peggy , Timper Patricia , Holbrook C. Corley , Jackson Scott A. , Bertioli David J. , Leal-Bertioli Soraya C. M. 
Published: November 2019

AbstractRoot-knot nematode is a very destructive pathogen, to which most peanut cultivars are highly susceptible. Strong resistance is present in the wild diploid peanut relatives. Previously, QTLs controlling nematode resistance were identified on chromosomes A02, A04 and A09 of Arachis stenosperma. Here, to study the inheritance of these resistance alleles within the genetic background of tetraploid peanut, an F2 population was developed from a cross between peanut and an induced allotetraploid that incorporated A. stenosperma, [Arachis batizocoi x A. stenosperma]4×. This population was genotyped using a SNP array and phenotyped for nematode resistance. QTL analysis allowed us to verify the major-effect QTL on chromosome A02 and a secondary QTL on A09, each contributing to a percentage reduction in nematode multiplication up to 98.2%. These were validated in selected F2:3 lines. The genome location of the large-effect QTL on A02 is rich in genes encoding TIR-NBS-LRR protein domains that are involved in plant defenses. We conclude that the strong resistance to RKN, derived from the diploid A. stenosperma, is transferrable and expressed in tetraploid peanut. Currently it is being used in breeding programs for introgressing a new source of nematode resistance and to widen the genetic basis of agronomically adapted peanut lines.
Efficient Control of THz Transmission of PEDOT:PSS with Resonant Nano-Metamaterials
Authors: Chaudhary Raghvendra P. , Das Bamadev , Oh Seugn In , Kim Dai-Sik 
Published: November 2019

AbstractNano-metamaterials designed to operate at a certain resonance frequency enhance the magnitude of terahertz (THz) wave transmission by three orders of magnitude or even more. In this pursuit, controlling magnitude of resonant transmission and tuning the resonance frequency is increasingly important for application in low power THz electronics and devices. THz optical properties of chemically doped poly(3,4‐ethylenedioxythiophene):poly(4‐styrenesulfonate) (PEDOT:PSS) have been studied, however its effect on the THz transmission properties in combination with nano-metamaterials have not yet been demonstrated. Here we demonstrate the efficient control over resonant THz transmission and tuning of resonance frequency of different nano-metamaterials using PEDOT:PSS, without any toxic chemical doping. By ease of simple solution processing with single step and drop-casting 10 μL aqueous solution of PEDOT:PSS on different nano-metamaterials with varied concentrations, we were able to dynamically control the THz transmission along with resonance frequency. This dynamic control of transmission and shift in resonance frequency can be attributed to improved conductivity of PEDOT:PSS and its interaction with strongly localized THz field of the metamaterial.
Mechanism and therapeutic effect of umbilical cord mesenchymal stem cells in inflammatory bowel disease
Authors: Pan Xing-hua , Li Qing-qing , Zhu Xiang-qing , Li Zi-an , Cai Xue-min , Pang Rong-qing , Ruan Guang-ping 
Published: November 2019

AbstractInflammatory bowel disease (IBD) is a persistent and chronic disease that is characterized by destructive gastrointestinal (GI) inflammation. Researchers are trying to identify and develop new and more effective treatments with no side effects. Acute and chronic mouse models of IBD were established using dextran sulfate sodium (DSS) solution. To evaluate the efficacy and mechanism, umbilical cord mesenchymal stem cells (UCMSCs) were obtained from Kunming (KM) mice and humans. In the chronic IBD study, the survival rates of the normal control, model, mouse UCMSC (mUCMSC) and human UCMSC (hUCMSC) groups were 100%, 40%, 86.7%, and 100%, respectively. The histopathological scores of the normal control, intraperitoneal injection, intravenous treatment, and model groups were 0.5 ± 0.30, 5.9 ± 1.10, 8.7 ± 1.39, and 8.8 ± 1.33 (p = 0.021). UCMSCs promoted the expression of the intestinal tight junction protein occludin, downregulated the protein expression of the autophagy marker LC3A/B in colon tissue, and upregulated the expression of VEGF-A and VEGFR-1 at the injured site. This study provides an experimental model for elucidating the therapeutic effects of UCMSCs in IBD. We provide a theoretical basis and method for the clinical treatment of IBD using UCMSCs.
Strain improvement of Escherichia coli K-12 for recombinant production of deuterated proteins
Authors: Kelpšas Vinardas , Wachenfeldt Claes von 
Published: November 2019

AbstractDeuterium isotope labelling is important for structural biology methods such as neutron protein crystallography, nuclear magnetic resonance and small angle neutron scattering studies of proteins. Deuterium is a natural low abundance stable hydrogen isotope that in high concentrations negatively affect growth of cells. The generation time for Escherichia coli K-12 in deuterated medium is substantially increased compared to cells grown in hydrogenated (protiated) medium. By using a mutagenesis plasmid based approach we have isolated an E. coli strain derived from E. coli K-12 substrain MG1655 that show increased fitness in deuterium based growth media, without general adaptation to media components. By whole-genome sequencing we identified the genomic changes in the obtained strain and show that it can be used for recombinant production of perdeuterated proteins in amounts typically needed for structural biology studies.
RSH enzyme diversity for (p)ppGpp metabolism in Phaeodactylum tricornutum and other diatoms
Authors: Avilan Luisana , Puppo Carine , Villain Adrien , Bouveret Emanuelle , Menand Benoit , Field Ben , Gontero Brigitte 
Published: November 2019

AbstractThe nucleotides guanosine tetraphosphate and pentaphosphate (together known as (p)ppGpp or magic spot) are produced in plant plastids from GDP/GTP and ATP by RelA-SpoT homologue (RSH) enzymes. In the model plant Arabidopsis (p)ppGpp regulates chloroplast transcription and translation to affect growth, and is also implicated in acclimation to stress. However, little is known about (p)ppGpp metabolism or its evolution in other photosynthetic eukaryotes. Here we studied (p)ppGpp metabolism in the marine diatom Phaeodactylum tricornutum. We identified three expressed RSH genes in the P. tricornutum genome, and determined the enzymatic activity of the corresponding enzymes by heterologous expression in bacteria. We showed that two P. tricornutum RSH are (p)ppGpp synthetases, despite substitution of a residue within the active site believed critical for activity, and that the third RSH is a bifunctional (p)ppGpp synthetase and hydrolase, the first of its kind demonstrated in a photosynthetic eukaryote. A broad phylogenetic analysis then showed that diatom RSH belong to novel algal RSH clades. Together our work significantly expands the horizons of (p)ppGpp signalling in the photosynthetic eukaryotes by demonstrating an unexpected functional, structural and evolutionary diversity in RSH enzymes from organisms with plastids derived from red algae.
Global ocean freshening, ocean mass increase and global mean sea level rise over 2005–2015
Authors: Llovel William , Purkey S. , Meyssignac B. , Blazquez A. , Kolodziejczyk N. , Bamber J. 
Published: November 2019

AbstractGlobal mean sea level has experienced an unabated rise over the 20th century. This observed rise is due to both ocean warming and increasing continental freshwater discharge. We estimate the net ocean mass contribution to sea level by assessing the global ocean salt budget based on the unprecedented amount of in situ data over 2005–2015. We obtain the ocean mass trends of 1.30 ± 1.13 mm · yr−1 (0–2000 m) and 1.55 ± 1.20 mm · yr−1 (full depth). These new ocean mass trends are smaller by 0.63–0.88 mm · yr−1 compared to the ocean mass trend estimated through the sea level budget approach. Our result provides an independent validation of Gravity Recovery And Climate Experiment (GRACE)-based ocean mass trend and, in addition, places an independent constraint on the combined Glacial Isostatic Adjustment – the Earth’s delayed viscoelastic response to the redistribution of mass that accompanied the last deglaciation- and geocenter variations needed to directly infer the ocean mass trend based on GRACE data.