bluuebunny/crossref_metadata_2025_split huggingface dataset:
On-line Ammonia Sensor and Invisible Security Ink by Fluorescent Zwitterionic Spirocyclic Meisenheimer Complex
Authors: Das Tanmay , Pramanik Apurba , Haldar Debasish 
Published: January 2017

AbstractAmmonia is not only a highly important gas for civilization but also contribute significantly for climate change and human health hazard. Highly sensitive ammonia sensor has been developed from a fluorescent zwitterionic spirocyclic Meisenheimer complex. Moreover, formation of this Meisenheimer complex can also be utilized for selective as well as naked eye instant detection of nitro aromatic explosive picric acid. The presence of a quaternary nitrogen atom directly attached to the spiro carbon is the unique feature of this Meisenheimer complex. This excellent photoluminescent (PL) Meisenheimer complex has two distinct stimuli responsive sites. One is sensitive towards acid while the other one is towards the base. These two positions can be modulated by adding one equivalent acid and one equivalent base to result two new products which are non fluorescent. One of these two non fluorescent species was found very exciting because of its UV/Vis transparency. Utilizing this concept we have fabricated an on-line sensor for measuring ammonia in dry or humid and condensing sewer air. The sensor was robust against ambient temperature and humidity variation. We have also developed an invisible ink from this Meisenheimer complex, with potential application for security purpose.
Urinary proteomics can define distinct diagnostic inflammatory arthritis subgroups
Authors: Siebert Stefan , Porter Duncan , Paterson Caron , Hampson Rosie , Gaya Daniel , Latosinska Agnieszka , Mischak Harald , Schanstra Joost , Mullen William , McInnes Iain 
Published: January 2017

AbstractCurrent diagnostic tests applied to inflammatory arthritis lack the necessary specificity to appropriately categorise patients. There is a need for novel approaches to classify patients with these conditions. Herein we explored whether urinary proteomic biomarkers specific for different forms of arthritis (rheumatoid arthritis (RA), psoriatic arthritis (PsA), osteoarthritis (OA)) or chronic inflammatory conditions (inflammatory bowel disease (IBD)) can be identified. Fifty subjects per group with RA, PsA, OA or IBD and 50 healthy controls were included in the study. Two-thirds of these populations were randomly selected to serve as a training set, while the remaining one-third was reserved for validation. Sequential comparison of one group to the other four enabled identification of multiple urinary peptides significantly associated with discrete pathological conditions. Classifiers for the five groups were developed and subsequently tested blind in the validation test set. Upon unblinding, the classifiers demonstrated excellent performance, with an area under the curve between 0.90 and 0.97 per group. Identification of the peptide markers pointed to dysregulation of collagen synthesis and inflammation, but also novel inflammatory markers. We conclude that urinary peptide signatures can reliably differentiate between chronic arthropathies and inflammatory conditions with discrete pathogenesis.
Prebiotic galactooligosaccharides activate mucin and pectic galactan utilization pathways in the human gut symbiont Bacteroides thetaiotaomicron
Authors: Lammerts van Bueren Alicia , Mulder Marieke , Leeuwen Sander van , Dijkhuizen Lubbert 
Published: January 2017

AbstractGalactooligosaccharides (GOS) are prebiotic carbohydrates that impart changes in the gut bacterial composition of formula-fed infants to more closely resemble that of breast-fed infants. Consuming human milk oligosaccharides (HMOs) provides specific bacterial strains with an advantage for colonizing the infant intestine. These same effects are seen in infants after GOS consumption, however GOS are very complex mixtures and the underlying molecular mechanisms of how GOS mimic HMOs are relatively unknown. Here we studied the effects of GOS utilization on a prominent gut symbiont, Bacteroides thetaiotaomicron, which has been previously shown to consume HMOs via mucin O-glycan degradation pathways. We show that several pathways for targeting O-mucin glycans are activated in B. thetaiotaomicron by GOS, as well as the galactan utilization sytem. Characterization of the endo-galactanase from this system identified activity on various longer GOS substrates while a subset of GOS compounds were identified as potential activators of mucin glycan metabolism in B. thetaiotaomicron. Our results show that GOS functions as an inducer of mucin-glycan pathways while providing a nutrient source in the form of β-(1 → 4)-galactan. These metabolic features of GOS mixtures may serve to explain the beneficial effects that are seen for GOS supplemented infant formula.
Low Temperature CO oxidation over Iron Oxide Nanoparticles Decorating Internal Structures of a Mesoporous Alumina
Authors: Kim Il Hee , Seo Hyun Ook , Park Eun Ji , Han Sang Wook , Kim Young Dok 
Published: January 2017

AbstractUsing a chemical vapor deposition method with regulated sample temperatures under ambient pressure conditions, we were able to fully decorate the internal structure of a mesoporous Al2O3 bead (~1 mm in particle diameter) with iron oxide nanoparticles (with a mean lateral size of less than 1 nm). The iron oxide-decorated Al2O3 showed a high CO oxidation reactivity, even at room temperature. Very little deactivation of the CO oxidation activity was observed with increasing reaction time at ~100 °C. Additionally, this catalyst showed high CO oxidation activity, even after annealing at ~900 °C under atmospheric conditions (i.e., the structure of the catalysts could be maintained under very harsh treatment conditions). We show that our catalysts have potential for application as oxidation catalysts in industrial processes due to the simplicity of their fabrication process as well as the high and stable catalytic performance.
Iron Oxide Films Prepared by Rapid Thermal Processing for Solar Energy Conversion
Authors: Wickman B. , Bastos Fanta A. , Burrows A. , Hellman A. , Wagner J. B. , Iandolo B. 
Published: January 2017

AbstractHematite is a promising and extensively investigated material for various photoelectrochemical (PEC) processes for energy conversion and storage, in particular for oxidation reactions. Thermal treatments during synthesis of hematite are found to affect the performance of hematite electrodes considerably. Herein, we present hematite thin films fabricated via one-step oxidation of Fe by rapid thermal processing (RTP). In particular, we investigate the effect of oxidation temperature on the PEC properties of hematite. Films prepared at 750 °C show the highest activity towards water oxidation. These films show the largest average grain size and the highest charge carrier density, as determined from electron microscopy and impedance spectroscopy analysis. We believe that the fast processing enabled by RTP makes this technique a preferred method for investigation of novel materials and architectures, potentially also on nanostructured electrodes, where retaining high surface area is crucial to maximize performance.
A Comprehensive Numerical Model for Simulating Fluid Transport in Nanopores
Authors: Zhang Yuan , Yu Wei , Sepehrnoori Kamy , Di Yuan 
Published: January 2017

AbstractSince a large amount of nanopores exist in tight oil reservoirs, fluid transport in nanopores is complex due to large capillary pressure. Recent studies only focus on the effect of nanopore confinement on single-well performance with simple planar fractures in tight oil reservoirs. Its impacts on multi-well performance with complex fracture geometries have not been reported. In this study, a numerical model was developed to investigate the effect of confined phase behavior on cumulative oil and gas production of four horizontal wells with different fracture geometries. Its pore sizes were divided into five regions based on nanopore size distribution. Then, fluid properties were evaluated under different levels of capillary pressure using Peng-Robinson equation of state. Afterwards, an efficient approach of Embedded Discrete Fracture Model (EDFM) was applied to explicitly model hydraulic and natural fractures in the reservoirs. Finally, three fracture geometries, i.e. non-planar hydraulic fractures, non-planar hydraulic fractures with one set natural fractures, and non-planar hydraulic fractures with two sets natural fractures, are evaluated. The multi-well performance with confined phase behavior is analyzed with permeabilities of 0.01 md and 0.1 md. This work improves the analysis of capillarity effect on multi-well performance with complex fracture geometries in tight oil reservoirs.
Quantifying the relative contributions of different solute carriers to aggregate substrate transport
Authors: Taslimifar Mehdi , Oparija Lalita , Verrey Francois , Kurtcuoglu Vartan , Olgac Ufuk , Makrides Victoria 
Published: January 2017

AbstractDetermining the contributions of different transporter species to overall cellular transport is fundamental for understanding the physiological regulation of solutes. We calculated the relative activities of Solute Carrier (SLC) transporters using the Michaelis-Menten equation and global fitting to estimate the normalized maximum transport rate for each transporter (Vmax). Data input were the normalized measured uptake of the essential neutral amino acid (AA) L-leucine (Leu) from concentration-dependence assays performed using Xenopus laevis oocytes. Our methodology was verified by calculating Leu and L-phenylalanine (Phe) data in the presence of competitive substrates and/or inhibitors. Among 9 potentially expressed endogenous X. laevis oocyte Leu transporter species, activities of only the uniporters SLC43A2/LAT4 (and/or SLC43A1/LAT3) and the sodium symporter SLC6A19/B0AT1 were required to account for total uptake. Furthermore, Leu and Phe uptake by heterologously expressed human SLC6A14/ATB0,+ and SLC43A2/LAT4 was accurately calculated. This versatile systems biology approach is useful for analyses where the kinetics of each active protein species can be represented by the Hill equation. Furthermore, its applicable even in the absence of protein expression data. It could potentially be applied, for example, to quantify drug transporter activities in target cells to improve specificity.
Epigenetic regulation of Plasmodium falciparum clonally variant gene expression during development in Anopheles gambiae
Authors: Gómez-Díaz Elena , Yerbanga Rakiswendé S. , Lefèvre Thierry , Cohuet Anna , Rowley M. Jordan , Ouedraogo Jean Bosco , Corces Victor G. 
Published: January 2017

AbstractP. falciparumphenotypic plasticity is linked to the variant expression of clonal multigene families such as thevargenes. We have examined changes in transcription and histone modifications that occur during sporogonic development ofP. falciparumin the mosquito host. Allvargenes are silenced or transcribed at low levels in blood stages (gametocyte/ring) of the parasite in the human host. After infection of mosquitoes, a singlevargene is selected for expression in the oocyst, and transcription of this gene increases dramatically in the sporozoite. The same PF3D7_1255200vargene was activated in 4 different experimental infections. Transcription of thisvargene during parasite development in the mosquito correlates with the presence of low levels of H3K9me3 at the binding site for the PF3D7_1466400 AP2 transcription factor. This chromatin state in the sporozoite also correlates with the expression of an antisense long non-coding RNA (lncRNA) that has previously been shown to promotevargene transcription during the intraerythrocytic cyclein vitro. Expression of both the sense protein-coding transcript and the antisense lncRNA increase dramatically in sporozoites. The findings suggest a complex process for the activation of a single particularvargene that involves AP2 transcription factors and lncRNAs.
MicroRNA-19b is a potential biomarker of increased myocardial collagen cross-linking in patients with aortic stenosis and heart failure
Authors: Beaumont Javier , López Begoña , Ravassa Susana , Hermida Nerea , San José Gorka , Gallego Idoia , Valencia Félix , Gómez-Doblas Juan José , de Teresa Eduardo , Díez Javier , González Arantxa 
Published: January 2017

AbstractThis study analyzed the potential associations of 7 myocardial fibrosis-related microRNAs with the quality of the collagen network (e.g., the degree of collagen fibril cross-linking or CCL) and the enzyme lysyl oxidase (LOX) responsible for CCL in 28 patients with severe aortic stenosis (AS) of whom 46% had a diagnosis of chronic heart failure (HF). MicroRNA expression was analyzed in myocardial and blood samples. From the studied microRNAs only miR-19b presented a direct correlation (p < 0.05) between serum and myocardium. Compared to controls both myocardial and serum miR-19b were reduced (p < 0.01) in AS patients. In addition, miR-19b was reduced in the myocardium (p < 0.01) and serum (p < 0.05) of patients with HF compared to patients without HF. Myocardial and serum miR-19b were inversely correlated (p < 0.05) with LOX, CCL and LV stiffness in AS patients. In in vitro studies miR-19b inhibition increased (p < 0.05) connective tissue growth factor protein and LOX protein expression in human fibroblasts. In conclusion, decreased miR-19b may be involved in myocardial LOX up-regulation and excessive CCL, and consequently increased LV stiffness in AS patients, namely in those with HF. Serum miR-19b can be a biomarker of these alterations of the myocardial collagen network in AS patients, particularly in patients with HF.
Intraarterial route increases the risk of cerebral lesions after mesenchymal cell administration in animal model of ischemia
Authors: Argibay Bárbara , Trekker Jesse , Himmelreich Uwe , Beiras Andrés , Topete Antonio , Taboada Pablo , Pérez-Mato María , Vieites-Prado Alba , Iglesias-Rey Ramón , Rivas José , Planas Anna M. , Sobrino Tomás , Castillo José , Campos Francisco 
Published: January 2017

AbstractMesenchymal stem cells (MSCs) are a promising clinical therapy for ischemic stroke. However, critical parameters, such as the most effective administration route, remain unclear. Intravenous (i.v.) and intraarterial (i.a.) delivery routes have yielded varied outcomes across studies, potentially due to the unknown MSCs distribution. We investigated whether MSCs reached the brain following i.a. or i.v. administration after transient cerebral ischemia in rats, and evaluated the therapeutic effects of both routes. MSCs were labeled with dextran-coated superparamagnetic nanoparticles for magnetic resonance imaging (MRI) cell tracking, transmission electron microscopy and immunohistological analysis. MSCs were found in the brain following i.a. but not i.v. administration. However, the i.a. route increased the risk of cerebral lesions and did not improve functional recovery. The i.v. delivery is safe but MCS do not reach the brain tissue, implying that treatment benefits observed for this route are not attributable to brain MCS engrafting after stroke.
Differential susceptibility and maturation of thymocyte subsets during Salmonella Typhimurium infection: insights on the roles of glucocorticoids and Interferon-gamma
Authors: Majumdar Shamik , Deobagkar-Lele Mukta , Adiga Vasista , Raghavan Abinaya , Wadhwa Nitin , Ahmed Syed Moiz , Rananaware Supriya Rajendra , Chakraborty Subhashish , Joy Omana , Nandi Dipankar 
Published: January 2017

AbstractThe thymus is known to atrophy during infections; however, a systematic study of changes in thymocyte subpopulations has not been performed. This aspect was investigated, using multi-color flow cytometry, during oral infection of mice withSalmonellaTyphimurium (S. Typhimurium). The major highlights are: First, a block in the developmental pathway of CD4−CD8−double negative (DN) thymocytes is observed. Second, CD4+CD8+double positive (DP) thymocytes, mainly in the DP1 (CD5loCD3lo) and DP2 (CD5hiCD3int), but not DP3 (CD5intCD3hi), subsets are reduced. Third, single positive (SP) thymocytes are more resistant to depletion but their maturation is delayed, leading to accumulation of CD24hiCD3hiSP. Kinetic studies during infection demonstrated differences in sensitivity of thymic subpopulations: Immature single positive (ISP) > DP1, DP2 > DN3, DN4 > DN2 > CD4+ > CD8+. Upon infection, glucocorticoids (GC), inflammatory cytokines, e.g. Ifnγ, etc are induced, which enhance thymocyte death. Treatment with RU486, the GC receptor antagonist, increases the survival of most thymic subsets during infection. Studies withIfnγ−/−mice demonstrated that endogenous Ifnγ produced during infection enhances the depletion of DN2-DN4 subsets, promotes the accumulation of DP3 and delays the maturation of SP thymocytes. The implications of these observations on host cellular responses during infections are discussed.
Role of molecular conformations in rubrene polycrystalline films growth from vacuum deposition at various substrate temperatures
Authors: Lin Ku-Yen , Wang Yan-Jun , Chen Ko-Lun , Ho Ching-Yuan , Yang Chun-Chuen , Shen Ji-Lin , Chiu Kuan-Cheng 
Published: January 2017

AbstractWe report on the optical and structural characterization of rubrene polycrystalline films fabricated from vacuum deposition with various substrate temperatures (Tsub). Depending on Tsub, the role of twisted and planar rubrene conformational isomers on the properties of rubrene films is focused. The temperature (T)-dependent inverse optical transmission (IOT) and photoluminescence (PL) spectra were performed on these rubrene films. The origins of these IOT and PL peaks are explained in terms of the features from twisted and planar rubrene molecules and of the band characteristics from rubrene molecular solid films. Here, two rarely reported weak-peaks at 2.431 and 2.605 eV were observed from IOT spectra, which are associated with planar rubrene. Besides, the T-dependence of optical bandgap deduced from IOT spectra is discussed with respect to Tsub. Together with IOT and PL spectra, for Tsub > 170 °C, the changes in surface morphology and unit cell volume were observed for the first time, and are attributed to the isomeric transformation from twisted to planar rubrenes during the deposition processes. Furthermore, a unified schematic diagram in terms of Frenkel exciton recombination is suggested to explain the origins of the dominant PL peaks performed on these rubrene films at 15 K.
High-molecular-weight hyaluronic acid attenuated matrix metalloproteinase-1 and -3 expression via CD44 in tendinopathy
Authors: Wu Po-Ting , Kuo Li-Chieh , Su Fong-Chin , Chen Shih-Yao , Hsu Tai-I , Li Chung-Yi , Tsai Kuen-Jer , Jou I-Ming 
Published: January 2017

AbstractEvidence indicates that hyaluronic acid (HA) mitigates tendinopathy, but the effect of molecular weight is unclear. We investigated the effects of different concentrations and different molecular weights of HA (350 kDa, 1500 kDa, and 3000 kDa) on matrix metalloproteinase (MMP)-1 and -3 expression in IL-1β-stimulated rat tenocytes, and on their dynamic expression in peritendinous effusion from patients with long head of biceps (LHB) tendinopathy after high-molecular-weight (HMW)-HA treatments. Reverse transcription PCR, real-time PCR, and ELISA were used to determine MMP-1 and -3expression. Because CD44 was clearly expressed in the plasma membranes of cultured tenocytes, OX-50, a CD44 antagonist, was used to inhibit CD44 to evaluate the HA mechanism. HA (3000 kDa) significantly (p < 0.001) downregulated the mRNA and protein expression of MMP-1 and -3 in IL-1β-stimulated tenocytes. Its attenuating effects were dose-dependent (p < 0.01). In OX-50-pretreated cells, the mRNA expression of CD44 was not significantly altered, but the mRNA expression of MMP-1 and -3 was significantly upregulated. Visual analogue scale scores were significantly lower, and MMP-1 and -3 expression was significantly (p < 0.05) lower one month posttreatment. HMW-HA attenuated tendinopathy by downregulating MMP-1 and -3 expression. Inhibiting CD44 blocked the effects of HMW-HA.
Excessive serial verb construction
Authors: Fan Ying 
Published: January 2017

Abstract
This paper identifies a distinct serial verb construction in Mandarin Chinese: the Excessive serial verb construction. This
construction exhibits formal similarity to the Resultative serial verb construction, since both of them involve adjacent unmarked
verbs. Despite the similarity, the former construction differs from the latter most evidently in that it conveys an excessive
meaning rather than a resultative meaning. This paper proposes that there is a syntactic difference between the two constructions.
In contrast to the tight structure in the Resultative serial verb construction, which can be represented as S[vp V1 V2]
le. The Excessive serial verb construction has a looser structure, which is structurally S[[vpV1] [vp
V2-le]]. With respect to diagnostics of constituency, the two constructions behave in different ways. This
paper further argues that correlating with a distinct structure, the Excessive serial verb construction requires obligatory
topicalization of its undergoer argument, a phenomenon that is not observed in the Resultative serial verb construction. This
study thus contributes to representing the interaction between the semantic properties – in particular, the function of
le in the two constructions – and the syntactic properties.
Darwin: A Hardware-acceleration Framework for Genomic Sequence Alignment
Authors: Turakhia Yatish , Zheng Kevin Jie , Bejerano Gill , Dally William J. 
Published: January 2017

ABSTRACTGenomics is set to transform medicine and our understanding of life in fundamental ways. But the growth in genomics data has been overwhelming - far outpacing Moore’s Law. The advent of third generation sequencing technologies is providing new insights into genomic contribution to diseases with complex mutation events, but have prohibitively high computational costs. Over 1,300 CPU hours are required to align reads from a 54× coverage of the human genome to a reference (estimated using [1]), and over 15,600 CPU hours to assemble the readsde novo[2]. This paper proposes “Darwin” - a hardware-accelerated framework for genomic sequence alignment that, without sacrificing sensitivity, provides 125× and 15.6× speedup over the state-of-the-art software counterparts for reference-guided andde novoassembly of third generation sequencing reads, respectively. For pairwise alignment of sequences, Darwin is over 39,000× more energy-efficient than software. Darwin uses (i) a novel filtration strategy, called D-SOFT, to reduce the search space for sequence alignment at high speed, and (ii) a hardware-accelerated version of GACT, a novel algorithm to generate near-optimal alignments of arbitrarily long genomic sequences using constant memory for trace-back. Darwin is adaptable, with tunable speed and sensitivity to match emerging sequencing technologies and to meet the requirements of genomic applications beyond read assembly.