bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation and use of disaccharides as energy source in protein-free mammalian cell cultures
Authors: Leong Dawn Sow Zong , Tan Janice Gek Ling , Chin Christine Lin , Mak Shi Ya , Ho Ying Swan , Ng Say Kong 
Published: March 2017

AbstractMammalian cells are generally considered to be unable to utilize polysaccharides for cell growth because the phospholipid bilayer in the cell membrane has very low permeability to sugars. With the recent discovery of the only known animal disaccharide transporter, a sucrose transporter, we considered the potential use of polysaccharides as energy source, because that can impact biopharmaceutical manufacturing by potentially increasing carbohydrate loading in the culture medium and decreasing lactate accumulation. In this study, we found that mammalian cells can utilize maltose for growth in the absence of glucose and successfully adapted CHO-K1, CHO-DG44 and HEK293 cells to grow in glucose-free, maltose-containing serum-free protein-free media. We then cultivated a non-adapted CHO-K1 producer cell line in media containing both glucose and maltose to show that the cells can utilize maltose in a biphasic manner, that maltose enters the cells, and that maltose utilization only took place in the presence of the cells. This is the first report of a protein-free mammalian cell culture using a disaccharide as energy source.
Specialist nectar-yeasts decline with urbanization in Berlin
Authors: Wehner Jeannine , Mittelbach Moritz , Rillig Matthias C. , Verbruggen Erik 
Published: March 2017

AbstractNectar yeasts are common inhabitants of insect-pollinated flowers but factors determining their distribution are not well understood. We studied the influence of host identity, environmental factors related to pollution/urbanization, and the distance to a target beehive on local distribution of nectar yeasts within Robinia pseudoacacia L. and Tilia tomentosa Moench in Berlin, Germany. Nectar samples of six individuals per species were collected at seven sites in a 2 km radius from each target beehive and plated on YM-Agar to visualise the different morphotypes, which were then identified by sequencing a section of the 26S rDNA gene. Multivariate linear models were used to analyze the effects of all investigated factors on yeast occurrence per tree. Yeast distribution was mainly driven by host identity. The influence of the environmental factors (NO2, height of construction, soil sealing) strongly depended on the radius around the tree, similar to the distance of the sampled beehive. Incidence of specialist nectar-borne yeast species decreased with increasing pollution/urbanization index. Given that specialist yeast species gave way to generalist yeasts that have a reduced dependency on pollinators for between-flower dispersal, our results indicate that increased urbanization may restrict the movement of nectar-specialized yeasts, via limitations of pollinator foraging behavior.
Identification and evolution of a plant cell wall specific glycoprotein glycosyl transferase, ExAD
Authors: Møller Svenning Rune , Yi Xueying , Velásquez Silvia Melina , Gille Sascha , Hansen Pernille Louise Munke , Poulsen Christian P. , Olsen Carl Erik , Rejzek Martin , Parsons Harriet , Yang Zhang , Wandall Hans H. , Clausen Henrik , Field Robert A. , Pauly Markus , Estevez Jose M. , Harholt Jesper , Ulvskov Peter , Petersen Bent Larsen 
Published: March 2017

AbstractExtensins are plant cell wall glycoproteins that act as scaffolds for the deposition of the main wall carbohydrate polymers, which are interlocked into the supramolecular wall structure through intra- and inter-molecular iso-di-tyrosine crosslinks within the extensin backbone. In the conserved canonical extensin repeat, Ser-Hyp4, serine and the consecutive C4-hydroxyprolines (Hyps) are substituted with an α-galactose and 1–5 β- or α-linked arabinofuranoses (Arafs), respectively. These modifications are required for correct extended structure and function of the extensin network. Here, we identified a single Arabidopsis thaliana gene, At3g57630, in clade E of the inverting Glycosyltransferase family GT47 as a candidate for the transfer of Araf to Hyp-arabinofuranotriose (Hyp-β1,4Araf-β1,2Araf-β1,2Araf) side chains in an α-linkage, to yield Hyp-Araf4 which is exclusively found in extensins. T-DNA knock-out mutants of At3g57630 showed a truncated root hair phenotype, as seen for mutants of all hitherto characterized extensin glycosylation enzymes; both root hair and glycan phenotypes were restored upon reintroduction of At3g57630. At3g57630 was named Extensin Arabinose Deficient transferase, ExAD, accordingly. The occurrence of ExAD orthologs within the Viridiplantae along with its’ product, Hyp-Araf4, point to ExAD being an evolutionary hallmark of terrestrial plants and charophyte green algae.
Argininosuccinate Synthase 1-Deficiency Enhances the Cell Sensitivity to Arginine through Decreased DEPTOR Expression in Endometrial Cancer
Authors: Ohshima Kenji , Nojima Satoshi , Tahara Shinichiro , Kurashige Masako , Hori Yumiko , Hagiwara Kohei , Okuzaki Daisuke , Oki Shinya , Wada Naoki , Ikeda Jun-ichiro , Kanai Yoshikatsu , Morii Eiichi 
Published: March 2017

AbstractArgininosuccinate synthetase 1 (ASS1) is a rate-limiting enzyme in arginine biosynthesis. Although ASS1 expression levels are often reduced in several tumors and low ASS1 expression can be a poor prognostic factor, the underlying mechanism has not been elucidated. In this study, we reveal a novel association between ASS1 and migration/invasion of endometrial tumors via regulation of mechanistic target of rapamycin complex (mTORC) 1 signaling. ASS1-knockout cells showed enhanced migration and invasion in response to arginine following arginine starvation. In ASS1-knockout cells, DEPTOR, an inhibitor of mTORC1 signal, was downregulated and mTORC1 signaling was more activated in response to arginine. ASS1 epigenetically enhanced DEPTOR expression by altering the histone methylation. Consistent with these findings, tumor cells at the invasive front of endometrioid carcinoma cases showed lower ASS1 and DEPTOR expression. Our findings suggest that ASS1 levels in each tumor cell are associated with invasion capability in response to arginine within the tumor microenvironment through mTORC1 signal regulation.
Antibody-dependent-cellular-cytotoxicity-inducing antibodies significantly affect the post-exposure treatment of Ebola virus infection
Authors: Liu Qiang , Fan Changfa , Li Qianqian , Zhou Shuya , Huang Weijin , Wang Lan , Sun Chunyun , Wang Meng , Wu Xi , Ma Jian , Li Baowen , Xie Liangzhi , Wang Youchun 
Published: March 2017

AbstractPassive immunotherapy with monoclonal antibodies (mAbs) is an efficacious treatment for Ebola virus (EBOV) infections in animal models and humans. Understanding what constitutes a protective response is critical for the development of novel therapeutic strategies. We generated an EBOV-glycoprotein-pseudotyped Human immunodeficiency virus to develop sensitive neutralizing and antibody-dependent cellular cytotoxicity (ADCC) assays as well as a bioluminescent-imaging-based mouse infection model that does not require biosafety level 4 containment. The in vivo treatment efficiencies of three novel anti-EBOV mAbs at 12 h post-infection correlated with their in vitro anti-EBOV ADCC activities, without neutralizing activity. When they were treated with these mAbs, natural killer cell (NK)-deficient mice had lower viral clearance than WT mice, indicating that the anti-EBOV mechanism of the ADCC activity of these mAbs is predominantly mediated by NK cells. One potent anti-EBOV mAb (M318) displayed unprecedented neutralizing and ADCC activities (neutralization IC50, 0.018 μg/ml; ADCC EC50, 0.095 μg/ml). These results have important implications for the efficacy of antiviral drugs and vaccines as well as for pathogenicity studies of EBOV.
Facile Fabrication of Platinum-Cobalt Alloy Nanoparticles with Enhanced Electrocatalytic Activity for a Methanol Oxidation Reaction
Authors: Huang Huihong , Hu Xiulan , Zhang Jianbo , Su Nan , Cheng JieXu 
Published: March 2017

AbstractDecreasing the cost associated with platinum-based catalysts along with improving their catalytic properties is a major challenge for commercial direct methanol fuel cells. In this work, a simple and facile strategy was developed for the more efficient preparation of multi-walled carbon nanotube (MWCNT) -supported Pt/CoPt composite nanoparticles (NPs) via solution plasma sputtering with subsequent thermal annealing. Quite different from general wet synthesis methods, Pt/CoPt composite NPs were directly derived from metal wire electrodes without any additions. The obtained Pt/CoPt/MWCNTs composite catalysts exhibited tremendous improvement in the electro-oxidation of methanol in acidic media with mass activities of 1719 mA mg−1Pt. This value is much higher than that of previous reports of Pt-Co alloy and commercial Pt/C (3.16 times) because of the many active sites and clean surface of the catalysts. The catalysts showed good stability due to the special synergistic effects of the CoPt alloy. Pt/CoPt/MWCNTs can be used as a promising catalyst for direct methanol fuel cells. In addition, this solution plasma sputtering-assisted synthesis method introduces a general and feasible route for the synthesis of binary alloys.
A novel pathway for amyloids self-assembly in aggregates at nanomolar concentration mediated by the interaction with surfaces
Authors: Banerjee Siddhartha , Hashemi Mohtadin , Lv Zhengjian , Maity Sibaprasad , Rochet Jean-Christophe , Lyubchenko Yuri L. 
Published: March 2017

AbstractA limitation of the amyloid hypothesis in explaining the development of neurodegenerative diseases is that the level of amyloidogenic polypeptide in vivo is below the critical concentration required to form the aggregates observed in post-mortem brains. We discovered a novel, on-surface aggregation pathway of amyloidogenic polypeptide that eliminates this long-standing controversy. We applied atomic force microscope (AFM) to demonstrate directly that on-surface aggregation takes place at a concentration at which no aggregation in solution is observed. The experiments were performed with the full-size Aβ protein (Aβ42), a decapeptide Aβ(14-23) and α-synuclein; all three systems demonstrate a dramatic preference of the on-surface aggregation pathway compared to the aggregation in the bulk solution. Time-lapse AFM imaging, in solution, show that over time, oligomers increase in size and number and release in solution, suggesting that assembled aggregates can serve as nuclei for aggregation in bulk solution. Computational modeling performed with the all-atom MD simulations for Aβ(14-23) peptide shows that surface interactions induce conformational transitions of the monomer, which facilitate interactions with another monomer that undergoes conformational changes stabilizing the dimer assembly. Our findings suggest that interactions of amyloidogenic polypeptides with cellular surfaces play a major role in determining disease onset.
Low phonon energies and wideband optical windows of La2O3-Ga2O3 glasses prepared using an aerodynamic levitation technique
Authors: Yoshimoto Kohei , Masuno Atsunobu , Ueda Motoi , Inoue Hiroyuki , Yamamoto Hiroshi , Kawashima Tastunori 
Published: March 2017

AbstractxLa2O3-(100 − x)Ga2O3 binary glasses were synthesized by an aerodynamic levitation technique. The glass-forming region was found to be 20 ≤ x ≤ 57. The refractive indices were greater than 1.92 and increased linearly with increasing x. The polarizabilities of oxide ions were estimated to be 2.16–2.41 Å3, indicating that the glasses were highly ionic. The glasses were transparent over a very wide range from the ultraviolet to the mid-infrared region. The widest transparent window among the oxide glasses was from 270 nm to 10 μm at x = 55. From the Raman scattering spectra, a decrease in bridging oxide ions and an increase in non-bridging oxide ions were confirmed to occur with increasing La2O3 content. The maximum phonon energy was found to be approximately 650 cm−1, being one of the lowest among oxide glasses. These results show that La2O3-Ga2O3 binary glasses should be promising host materials for optical applications such as lenses, windows, and filters over a very wide wavelength range.
Visual deprivation selectively reshapes the intrinsic functional architecture of the anterior insula subregions
Authors: Liu Lihua , Yuan Congcong , Ding Hao , Xu Yongjie , Long Miaomiao , Li YanJun , Liu Yong , Jiang Tianzi , Qin Wen , Shen Wen , Yu Chunshui 
Published: March 2017

AbstractThe anterior insula (AI) is the core hub of salience network that serves to identify the most relevant stimuli among vast sensory inputs and forward them to higher cognitive regions to guide behaviour. As blind subjects were usually reported with changed perceptive abilities for salient non-visual stimuli, we hypothesized that the resting-state functional network of the AI is selectively reorganized after visual deprivation. The resting-state functional connectivity (FC) of the bilateral dorsal and ventral AI was calculated for twenty congenitally blind (CB), 27 early blind (EB), 44 late blind (LB) individuals and 50 sighted controls (SCs). The FCs of the dorsal AI were strengthened with the dorsal visual stream, while weakened with the ventral visual stream in the blind than the SCs; in contrast, the FCs of the ventral AI of the blind was strengthened with the ventral visual stream. Furthermore, these strengthened FCs of both the dorsal and ventral AI were partially negatively associated with the onset age of blindness. Our result indicates two parallel pathways that selectively transfer non-visual salient information between the deprived “visual” cortex and salience network in blind subjects.
High‐sensitivity structure for the measurement of complex permittivity based on SIW
Authors: Yang Xiaoqing , Xin Lei , Jiao Xingmin , Zhou Peiping , Wu Shiyue , Huang Kama 
Published: March 2017

In this study, a substrate integrated waveguide (SIW) combined with complementary split‐ring resonator (CSRR) structure is proposed for high‐sensitivity measurement of complex permittivity of low loss material at 2.45 GHz. The simulated results demonstrated that the small changes can be sensed through loading the CSRR structure on both sides of SIW. Then, the experiments are performed on various dielectric samples to validate the proposed structure by measuring the particulate samples with different moisture contents and solution samples in different mixed volume ratio. The measured results show that the sensitivity of the proposed SIW with CSRR structure is always higher than the structure without CSRR. Furthermore, neural network based on actual experimental scattering parameters is used for obtaining the permittivity of samples under test. The experimental values agree well with the theoretical values, and the relative errors of and are <5 and 10%.
Point-of-Care Coagulation Testing in Cardiac Surgery
Authors: Tanaka Kenichi , Bolliger Daniel 
Published: March 2017

AbstractBleeding complications after cardiac surgery are common and are associated with increased morbidity and mortality. Their etiology is multifactorial, and treatment decisions are time sensitive. Point-of-care (POC) testing has an advantage over standard laboratory tests for faster turn-around times, and timely decision on coagulation intervention(s). The most common POC coagulation testing is the activated clotting time (ACT), used to monitor heparin therapy while on cardiopulmonary bypass. Viscoelastic coagulation tests including thromboelastometry (ROTEM) and thromboelastography (TEG) have been recommended for the treatment of postoperative bleeding after cardiac surgery because the ROTEM/TEG-guided treatment algorithms reduced the use of blood products. Other POC tests are commercially available, but there is sparse evidence for their routine use in cardiac surgery. These devices include heparin management systems, POC prothrombin time and activated partial thromboplastin time, POC fibrinogen assay, and whole blood platelet function tests. There are multiple confounding elements and conditions associated with cardiac surgery, which can significantly alter test results. Anemia and thrombocytopenia are regularly associated with deviations in many POC devices. In summary, POC coagulation testing allows for rapid clinical decisions in hematological interventions, and, when used in conjunction with a proper transfusion algorithm, may reduce blood product usage, and potentially complications associated with blood transfusion.
Percutaneous Management of Malignant Biliary Strictures: Current Status and Future Directions
Authors: Attaya Mohammed , Attaya Hosam , Thabet Ashraf 
Published: March 2017

AbstractVarious minimally invasive percutaneous interventions may be performed for the treatment and management of malignant biliary obstruction. The types of percutaneous interventions include percutaneous transhepatic biliary drainage, percutaneous cholecystostomy, and biliary stent placement. Biliary stents have undergone continued evolution in design to prolong patency, increase cost-effectiveness, improve patient survival, and quality of life. Furthermore, investigational techniques, such as radiofrequency ablation, intraluminal brachytherapy, and photodynamic therapy promise new technologies in the field of biliary intervention. This review focuses on the current status of percutaneous therapies for malignant biliary strictures and obstruction.
Approximate solutions for the nonlinear duffing oscillator with an external force
Authors: Kirinin Jutamas , Mahithithummath Kanokwan , Kongsawasdi Narisara , Kasemsuwan Jaipong 
Published: March 2017

Abstract
This paper is concerned with a finding of an approximate solution to the Duffing oscillator with a linear external force using a modified differential transform method (MDTM) and Runge-Kutta-Nystrom (RKN) method. The results obtained from the two methods are then numerically and graphically compared. We found that both results are close to one another when an amplitude and frequency of external forces are very small. However, both results are quite different when the amplitude and frequency of external forces are large. Their results are in agreement with the phase plane diagram which demonstrates a stable equilibrium point for both methods in case of small amplitude and frequency of external force. However, for large amplitude and frequency of external forces, only MDTM shows the stable equilibrium point.
Quality Improvement in Pediatric Endoscopy
Authors: Kramer Robert E. , Walsh Catharine M. , Lerner Diana G. , Fishman Douglas S. 
Published: March 2017

ABSTRACTThe current era of healthcare reform emphasizes the provision of effective, safe, equitable, high‐quality, and cost‐effective care. Within the realm of gastrointestinal endoscopy in adults, renewed efforts are in place to accurately define and measure quality indicators across the spectrum of endoscopic care. In pediatrics, however, this movement has been less‐defined and lacks much of the evidence‐base that supports these initiatives in adult care. A need, therefore, exists to help define quality metrics tailored to pediatric practice and provide a toolbox for the development of robust quality improvement (QI) programs within pediatric endoscopy units. Use of uniform standards of quality reporting across centers will ensure that data can be compared and compiled on an international level to help guide QI initiatives and inform patients and their caregivers of the true risks and benefits of endoscopy. This report is intended to provide pediatric gastroenterologists with a framework for the development and implementation of endoscopy QI programs within their own centers, based on available evidence and expert opinion from the members of the NASPGHAN Endoscopy Committee. This clinical report will require expansion as further research pertaining to endoscopic quality in pediatrics is published.
Multiplexed sgRNA Expression Allows Versatile Single Non-repetitive DNA Labeling and Endogenous Gene Regulation
Authors: Shao Shipeng , Chang Lei , Sun Yuao , Hou Yingping , Fan Xiaoying , Sun Yujie 
Published: March 2017

ABSTRACTThe CRISPR/Cas9 system has made significant contribution to genome editing, gene regulation and chromatin studies in recent years. High-throughput and systematic investigations into the multiplexed biological systems and disease conditions require simultaneous expression and coordinated functioning of multiple sgRNAs. However, current co-transfection based sgRNA co-expression systems remain poorly efficient and virus-based transfection approaches are relatively costly and labor intensive. Here we established a vector-independent method allowing multiple sgRNA expression cassettes to be assembled in series into a single plasmid. This synthetic biology-based strategy excels in its efficiency, controllability and scalability. Taking the flexibility advantage of this all-in-one sgRNA expressing system, we further explored its applications in single non-repetitive genomic locus imaging as well as coordinated gene regulation in live cells. With its strong potency, our method will greatly facilitate the understandings in genome structure, function and dynamics, and will contribute to the systemic investigations into complex physiological and pathological conditions.
Squeakr: An Exact and Approximatek-mer Counting System
Authors: Pandey Prashant , Bender Michael A. , Johnson Rob , Patro Rob 
Published: March 2017

AbstractMotivationk-mer-based algorithms have become increasingly popular in the processing of high-throughput sequencing (HTS) data. These algorithms span the gamut of the analysis pipeline fromk-mer counting (e.g., for estimating assembly parameters), to error correction, genome and transcriptome assembly, and even transcript quantification. Yet, these tasks often use very differentk-mer representations and data structures. In this paper, we set forth the fundamental operations for maintaining multisets ofk-mers and classify existing systems from a data-structural perspective. We then show how to build ak-mer-counting and multiset-representation system using the counting quotient filter (CQF), a feature-rich approximate membership query (AMQ) data structure. We introduce thek-mer-counting/querying system Squeakr (Simple Quotient filter-based Exact and Approximate Kmer Representation), which is based on the CQF. This off-the-shelf data structure turns out to be an efficient (approximate or exact) representation for sets or multisets ofk-mers.ResultsSqueakr takes 2×−3;4.3× less time than the state-of-the-art to count and perform a random-point-query workload. Squeakr is memory-efficient, consuming 1.5X–4.3X less memory than the state-of-the-art. It offers competitive counting performance, and answers point queries (i.e. queries for the abundance of a particulark-mer) over an order-of-magnitude faster than other systems. The Squeakr representation of thek-mer multiset turns out to be immediately useful for downstream processing (e.g., de Bruijn graph traversal) because it supports fast queries and dynamick-mer insertion, deletion, and modification.Availabilityhttps://github.com/splatlab/squeakrContactppandey@cs.stonybrook.edu