bluuebunny/crossref_metadata_2025_split huggingface dataset:
Jetstream—Early operations performance, adoption, and impacts
Authors: Hancock David Y. , Stewart Craig A. , Vaughn Matthew , Fischer Jeremy , Lowe John Michael , Turner George , Swetnam Tyson L. , Chafin Tyler K. , Afgan Enis , Pierce Marlon E. , Snapp‐Childs Winona 
Published: September 2018

SummaryJetstream is a first of its kind system for the NSF — a distributed production cloud resource. We review the purpose for creating Jetstream, discuss Jetstream's key characteristics, describe our experiences from the first year of maintaining an OpenStack‐based cloud environment, and share some of the early scientific impacts achieved by Jetstream users. Jetstream offers a unique capability within the XSEDE‐supported US national cyberinfrastructure, delivering interactive virtual machines (VMs) via the Atmosphere interface. As a multi‐region deployment that operates as an integrated system, Jetstream is proving effective in supporting modes and disciplines of research traditionally underrepresented on larger XSEDE‐supported clusters and supercomputers. Already, Jetstream has been used to perform research and education in biology, biochemistry, atmospheric science, earth science, and computer science.
Concurrent agent‐based evolutionary computations as adaptive dataflows
Authors: Krzywicki Daniel , Faber Łukasz , Dębski Roman 
Published: September 2018

SummaryThis paper introduces a new formal description of the execution model for agent‐based computing systems in the form of an adaptive dataflow decoupled from the domain‐specific semantics of the computation. We show that the execution models studied in previous work can be unified in this common model. The parameters of the model such as queuing policies and granularity of the data in the flow are analyzed. Several queueing alternatives are benchmarked to demonstrate how they affect the efficiency of the computation. Using the example of a multi‐agent evolutionary optimisation problem solver, the new approach is shown to outperform the classic one. This proposed model is well suited to functional languages and can be easily mapped onto different classes of hardware – from simple single‐core computers to distributed environments.
Changes in serum afamin and vitamin E levels after selective LDL apheresis
Authors: Varga Viktória E. , Lőrincz Hajnalka , Szentpéteri Anita , Juhász Lilla , Seres Ildikó , Paragh György , Balla József , Paragh György , Harangi Mariann 
Published: September 2018

AbstractBackgroundAfamin is a plasma vitamin E‐binding glycoprotein partially associated with ApoA1‐containing high‐density lipoprotein (HDL) subfractions. In a previous study, the serum vitamin E decreased after low‐density lipoprotein (LDL) apheresis, while vitamin E/cholesterol ratio increased. We aimed to study the effect of LDL apheresis on serum afamin level.MethodsThe serum level of afamin and oxidized LDL were measured by enzyme‐linked immunosorbent assay in six severe heterozygous FH patients before and after their first LDL apheresis treatments and in seven healthy controls. We also investigated the changes in total cholesterol, LDL‐C, HDL‐C, ApoB, ApoA1, HDL subfractions, and α‐ and γ‐tocopherol levels during the treatment. HDL subfractions were detected by an electrophoretic method on polyacrylamide gel (Lipoprint). Serum α‐ and γ‐tocopherol levels were detected by gas chromatography‐mass spectrometry.ResultsThe first treatment sessions decreased serum afamin levels by an average of 9.4%. Total cholesterol, LDL‐C, HDL‐C and ApoA1 levels decreased by 52.6; 61.8; 10.5; and 14.1%, respectively. We found that α‐ and γ‐tocopherol levels markedly decreased (by 34.1 and 32.9%, respectively), while α‐ tocopherol/cholesterol and γ‐tocopherol/cholesterol ratios significantly increased (by 41.4 and 40.3%, respectively). Oxidized LDL levels significantly decreased. There was a shift toward the larger HDL subfractions.ConclusionLDL apheresis moderately decreases the circulating levels of afamin parallel to lowering HDL‐C and ApoA1 levels. Tocopherol levels decreases markedly compared to afamin levels, however, beneficial changes in vitamin E/cholesterol ratios, oxidized LDL levels and HDL subfraction distribution were detected. These additional effects of LDL apheresis may result in further cardiovascular risk reduction in FH patients.
A century of bacteriophage research and applications: impacts on biotechnology, health, ecology and the economy!
Authors: Vandamme Erick J , Mortelmans Kristien 
Published: September 2018

AbstractAbout a century ago, bacteriophages or phages – viruses that infect bacteria – were discovered and reported in the scientific literature. This review aims at a comprehensive survey of bacteriophage discovery, research and applications since the 1920s, and its impact on molecular biology, biotechnology, health, ecology and the economy. Phage therapy has been proven a valuable asset to deal with pathogenic bacterial infections since the early 1920s, and has been practiced ever since, especially in the former Soviet Union and in Eastern Europe. The Western world remained sceptical and resorted to the widespread use of antibiotics since the 1940s. Now that antibiotic resistance among pathogenic bacteria has spread alarmingly and few really novel antibiotic compounds are in the pipeline, renewed attention is being directed to the use of phages as antibacterial agents in medicine. Because of this renewed interest in phage therapy in the Western world, novel applications with phages are being pursued in the human health, environmental and the agri‐food sectors. This review will focus on (1) the history of early phage use and its successes and problems, (2) the study of phages as important tools in the development of molecular biology and biotechnology, (3) current developments in phage research including the use of phage endolysins for use in antibacterial treatment, (4) phage production systems including undesirable phage contamination of industrial fermentation processes based on bacteria, (5) recent applications in phage therapy and in phage‐based control, and (6) the roles of phages in nature and in the human gut. © 2018 Society of Chemical Industry
Comparison of Rossini–Rothwell and adaptive threshold‐hunting methods on the stability of TMS induced motor evoked potentials amplitudes
Authors: Dissanayaka Thusharika , Zoghi Maryam , Farrell Michael , Egan Gary , Jaberzadeh Shapour 
Published: September 2018

AbstractSeveral methods can be used to determine the resting motor threshold (RMT) and by that recording transcranial magnetic stimulation (TMS) induced motor evoked potentials (MEPs). However, no research has compared the test retest reliability of these methods. Thus, the aim of this study was to determine intra‐ and inter‐session reliability of Rossini–Rothwell (R–R) and parameter estimation by sequential testing (PEST) methods on TMS‐induced MEPs and comparison of these two methods on RMT. Twelve healthy individuals participated in this study three times (T1, T2 and T3) over two days. TMS was applied using both R–R and PEST to estimate RMT and average of 25 MEPs were acquired at each of the three time points. The intra‐class correlation coefficient indicated high intra‐session reliability in the MEP amplitudes for both methods (0.79 and 0.88, R–R and PEST respectively). The RMT and MEP amplitudes had higher inter‐session reliability in both methods (0.99 and 0.998, R–R and PEST respectively; 0.84 and 0.76, R–R and PEST respectively). There was no significant difference between methods for RMT at both T1 (maximum stimulator output of R–R vs. PEST, 33.7% ± 7.7% vs. 33.8% ± 7.6%, p = 0.75) and T3 (maximum stimulator output of R–R vs. PEST, 33.5% ± 7.3% vs. 33.7% ± 7.3%, p = 0.19). There was a significant positive correlation between the methods' estimates of RMT, with PEST requiring significantly fewer stimuli. This study shows that the R–R and PEST methods have high intra‐and inter‐session reliability and the same precision, with PEST having the advantage over R–R in speed of estimation of RMT.
Meta‐Dimethoxy‐Substituted Difluoroboron Dibenzoylmethane Poly(Lactic Acid) Nanoparticles for Luminescence Anisotropy
Authors: Zhuang Meng , Perkins Anna , DeRosa Christopher A. , Butler Tristan , Demas James N. , Fraser Cassandra L. 
Published: September 2018

AbstractDifluoroboron β‐diketonates derivatives are dyes with tunable fluorescence and room temperature phosphorescence when embedded in a rigid matrix such as poly(lactic acid) (PLA). Both fluorescence and phosphorescence are present in solid‐state PLA, enabling a variety of applications such as bio‐imaging and oxygen sensing. Here, a meta‐dimethoxy‐substituted difluoroboron dibenzoylmethane [BF2dbm(m‐OMe)2OH] is prepared, and two PLA polymers [BF2dbm(m‐OMe)2PLA] with different dye loadings are produced. Optical properties are studied in solution, and the emissions are environment sensitive. This is supported by density functional theory (DFT) calculations where intramolecular charge transfer is present and related to solvatochromism. Nanoparticles are fabricated with solvents of varied polarities via nanoprecipitation. Dynamic light scattering indicates dimethylformamide generates the smallest nanoparticles and tetrahydrofuran the largest. Luminescence polarization establishes that the absorbing and emitting dipoles are single axis and collinear. Förster resonance energy transfer within the nanoparticles is important and depends strongly on dye loadings.
Synthetic Approach of Thermally Tunable Nature‐Mimetic Polypeptides from N‐Protected Alternating Peptoids
Authors: Koyama Yasuhito , Ihsan Abu Bin , Gudeangadi Prashant Gopal 
Published: September 2018

AbstractA facile approach to synthesize nature‐mimetic polypeptides via the formation of N‐protected intermediates is developed. The approach is based on the use of stable and easily cleavable N‐(1‐p‐methoxyphenethyl) (MPE) group as a new N‐protecting group for an amide group. The MPE‐protected polypeptides are prepared in one‐pot via three‐component polycondensation using amino acid–free starting materials. Subsequent acidic treatment of the obtained polypeptides result in the perfect removal of MPE to give the nature‐mimetic polypeptides consisting of alternating peptide skeleton. The aqueous solutions of the nature‐mimetic polypeptides exhibit thermal responsivity depending on the structure of pendant functionalities.
Emission and Emissive Mechanism of Nonaromatic Oxygen Clusters
Authors: Wang Yunzhong , Bin Xin , Chen Xiaohong , Zheng Shuyuan , Zhang Yongming , Yuan Wang Zhang 
Published: September 2018

AbstractNonaromatic luminophores without remarkable conjugates have aroused great attention. Their emission mechanism, however, remains an open question. Meanwhile, previous studies generally focus on aliphatic amine and/or carbonyl‐containing systems; those with merely oxygen moieties (i.e., ether, hydroxyl) are scarcely touched. Recently, the clustering‐triggered emission (CTE) mechanism is proposed to rationalize the emission of nonconventional luminophores, according to which compounds bearing purely oxygen moieties can also be emissive. To check this conjecture, herein, both nonaromatic compound of xylitol and polymers of PEG and F127 are studied, which are found to be emissive in concentrated solutions and solids. Furthermore, cryogenic‐persistent phosphorescence of the compounds and even persistent room temperature phosphorescence of xylitol crystals are observed. Additionally, their potential application as Fe3+ sensors is demonstrated. These results not only verify the rationality of the CTE mechanism but also suggest the possibility to discover and design new luminophores according to it.
HMGA2 promotes intestinal tumorigenesis by facilitating MDM2‐mediated ubiquitination and degradation of p53
Authors: Wang Yuhong , Hu Lin , Wang Jian , Li Xiangwei , Sahengbieke Sana , Wu Jingjing , Lai Maode 
Published: September 2018

AbstractHigh mobility group A2 (HMGA2) is an architectural transcription factor that promotes human colorectal cancer (CRC) aggressiveness by modulating the transcription of target genes. The degradation of p53 is mediated by murine double minute 2 (MDM2) in a proteasome‐dependent manner. Here we report that HMGA2 promotes cell cycle progression and inhibits apoptosis in CRC cells in vitro. We also developed an intestinal epithelial cell‐specific Hmga2 knock‐in (KI) mouse model. It revealed that the Hmga2 KI promoted chemical carcinogen‐induced tumorigenesis in the intestine in vivo. In studying the underlying molecular mechanism, we found that HMGA2 formed a protein complex with p53. The tetramerization domain of p53 (amino acids 294–393) and the three AT‐hook domains (amino acids 1–83) of HMGA2 were responsible for their direct interaction. We also found that HMGA2 directly bound to MDM2 and the central acidic and zinc finger domains of MDM2 (amino acids 111–360) were required for interaction with HMGA2. Furthermore, our results indicated that HMGA2 promoted MDM2‐mediated p53 ubiquitination and degradation. Interestingly, Hmga2 overexpression in Hmga2 KI mice resulted in an increase in the accumulation of ubiquitinated p53. In addition, in two large CRC cohorts, it was demonstrated that high HMGA2 expression was predictive of an adverse outcome in the p53‐negative subgroup of CRC patients. In summary, our data have established for the first time a novel mechanism by which HMGA2 functions with p53 and MDM2 to promote CRC progression. Copyright © 2018 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Primary renal angiosarcoma: A case report and literature review
Authors: Li Xiao li , Tian Xin , Guo Jin , Zhang Hong , Wang Shuang , Dai Shun dong 
Published: September 2018

AbstractKidney angiosarcomas usually metastasize from the skin, soft tissue, or visceral primary lesions, whereas primary renal angiosarcomas are rare. We report a case of primary renal angiosarcoma with morphological features similar to those of anastomosis hemangioma. Microscopically, there were multiple irregular anastomosing vascular spaces or channel‐like labyrinthine structures, and the tumor cells were positive for CD31, CD34, FLI‐1, PAX8, and vimentin; focally positive for factor VIII, CD10, and Ki‐67 (approximately 5%); and uniformly‐negative for CK, S‐100, and Melan‐A. The diagnosis of angiosarcoma depends on morphological and immunohistochemical examinations.
Do bromadiolone treatments to control grassland water voles (Arvicola scherman) affect small mustelid abundance?
Authors: Fernandez‐de‐Simon Javier , Coeurdassier Michael , Couval Geoffroy , Fourel Isabelle , Giraudoux Patrick 
Published: September 2018

ABSTRACTBackgroundThe use of pesticides can affect non‐target species by causing population declines through indirect intoxication. Small mustelids (SMs; weasels, Mustela nivalis L.; stoats, Mustela erminea L.) consume water voles (WVs, Arvicola scherman S.) and can be exposed to bromadiolone, an anticoagulant rodenticide used in some countries to reduce WV damage to grasslands. Here, we investigated whether bromadiolone affected SM abundance.ResultsWe monitored SM abundance using footprint tracking tunnels in spring and autumn at ten sites. Among these sites, four were treated with bromadiolone, while six were not treated. We found reduced SM abundance at these four sites from spring to autumn (treated sites, mean ± SE SM abundance change = −1.68 ± 0.42; untreated sites, 0.29 ± 0.25). Using a linear model, we observed that SM abundance decreased as a function of the quantity of bromadiolone applied during the 3 months before the autumn estimate. We found that WV abundance increased at treated sites (linear model, treated sites, mean ± SE WV abundance change = 1.4 ± 0.4; untreated sites, 0.33 ± 0.25). Thus, at treated sites, SM abundance declined despite increased food availability. By analyzing residues in vole livers and SM scats we showed that SMs may be exposed to bromadiolone at the sites where this compound was used.ConclusionThis study is the first to document the relationship between SM abundance and bromadiolone usage for small mammal control. Declines in SM abundance were observed at treated sites, where bromadiolone residue was found in SM scats. This correlative approach suggests that bromadiolone treatment may lead to seasonal SM declines and associated WV increases. © 2018 Society of Chemical Industry
Analyzing torquoselectivity in a series of unusual ring‐opening reactions through bond reactivity indices and the adaptive natural density partitioning method
Authors: Morales‐Bayuelo Alejandro , Sánchez‐Márquez Jesús , Jana Gourhari , Chattaraj Pratim Kumar 
Published: September 2018

AbstractIn this study, a theoretical analysis of the torquoselectivity in a set of unusual ring‐opening reactions (R1‐R5) is presented. To describe the mechanism of the reactions, a recent methodology has been used to estimate the electrophilicities of the natural bond orbitals of the reagents and has been complemented with a second‐order perturbation theory analysis. The adaptive natural density partitioning method has also been used to verify the results and conclusions of the analysis. The concordant results of the three methodologies provide us with a better understanding of the reaction mechanism involving the torquoselectivity. We also carried out the analysis in both directions of the reaction to verify the conclusions obtained.
Effect of water on the interfacial structures of room‐temperature ionic liquids
Authors: Kawada Shouhei , Kodama Eri , Sato Keisuke , Ogawa Shuhei , Watanabe Masaya , Okubo Hikaru , Sasaki Shinya 
Published: September 2018

The interfacial structures of cyano‐based room‐temperature ionic liquids play a very important role in reducing friction. However, the presence of water impairs their tribological performance. The interfacial structures and friction forces of 1‐ethyl‐3‐methylimidazolium dicyanamide, [EMIM][DCN], and the effect of water on these structures and forces were investigated using atomic force microscopy. In addition, the interaction of water and [EMIM][DCN] was evaluated using Fourier‐transform infrared (FT‐IR) spectroscopy. Multiple repulsive layers were observed in the [EMIM][DCN] solution. This solution showed low friction force because these repulsive layers worked as protective layers against friction. On the other hand, the specific repulsive layer characteristics of [EMIM][DCN] could not be observed in a [EMIM][DCN] + 2 wt% H2O solution. FT‐IR results indicated that the layer structure of [EMIM][DCN] was disturbed by the addition of H2O. Therefore, the solution containing water exhibited a high friction force.
Regulation of Human Airway Epithelial Tissue Stem Cell Differentiation by β-Catenin, P300, and CBP
Authors: Malleske Daniel T. , Hayes Don , Lallier Scott W. , Hill Cynthia L. , Reynolds Susan D. 
Published: September 2018

Abstract
The wingless/integrase-1 (WNT)/β-catenin signaling pathway is active in several chronic lung diseases including idiopathic pulmonary fibrosis, asthma, and chronic obstructive pulmonary disease. Although this WNT/β-catenin pathway activity is associated with an increase in mucus cell frequency and a decrease in ciliated cell frequency, a cause and consequence relationship between signaling and cell frequency has not been established. We previously demonstrated that genetic stabilization of β-catenin inhibited differentiation of mouse bronchiolar tissue stem cells (TSC). This study determined the effect of β-catenin and its co-factors P300 (E1A-binding protein, 300 kDa) and cAMP response element binding (CREB)-binding protein (CBP) on human bronchial epithelial TSC differentiation to mucus and ciliated cells. We developed a modified air–liquid interface (ALI) culture system in which mucus and ciliated cell frequency is similar. These cultures were treated with the β-catenin agonist CHIR99021 (CHIR) and antagonists to β-catenin (XAV939), P300 (IQ1), and CBP (ICG001). We report that human TSC differentiation to mucus and ciliated cells can be divided into two stages, specification and commitment. CHIR treatment inhibited mucus and ciliated cell commitment while XAV939 treatment demonstrated that β-catenin was necessary for mucus and ciliated cell specification. Additional studies demonstrate that a β-catenin/P300 complex promotes mucus cell specification and that β-catenin interacts with either P300 or CBP to inhibit ciliated cell commitment. These data indicate that activation of β-catenin-dependent signaling in chronic lung disease leads to changes in mucus and ciliated cell frequency and that P300 and CBP tune the β-catenin signal to favor mucus cell differentiation.
Human T-Lymphotropic Virus-1–Associated Myelopathy/Tropical Spastic Paraparesis Is Associated With Sexual Dysfunction in Infected Women of Reproductive Age
Authors: Lopes Martins Adenilda Lima , Rios Grassi Maria Fernanda , de Aquino Firmino Alisson , Lacerda Araujo Jean Paulo , Paixao Taiane Silva , Galvão-Castro Bernardo , Boa-Sorte Ney 
Published: September 2018

Abstract

Introduction
Human T-lymphotropic virus (HTLV)-1–associated myelopathy/tropical spastic paraparesis (HAM/TSP) is a neurological disorder that mostly affects women. This disease is characterized by a progressive loss of motor function and disruptions in sensory function in the lower limbs. HTLV-1 is also associated with isolated neurologic dysfunctions, overactive bladder, and erectile dysfunction. The occurrence of sexual dysfunction in HTLV-1–infected women remain unclear.

Aim
To investigate associations between HTLV-1 infection and sexual dysfunction in both asymptomatic infected women and those diagnosed with HAM/TSP compared with uninfected women.

Methods
HTLV-1–infected and uninfected women were assessed for sexual dysfunction using the Female Sexual Function Index instrument. Sexual dysfunction was considered if global Female Sexual Function Index scores were &lt;26.5. Crude and adjusted prevalence ratios (PR) with 95% CI were calculated to identify associations between sexual dysfunction (outcome) and HTLV infection status–asymptomatic or HAM/TSP (main exposure), compared with uninfected women, and adjusted by sociodemographic and/or clinical characteristics (covariables).

Results
HTLV-1–infected women (n = 72; 57 asymptomatic; 15 HAM/TSP) and HTLV-1 uninfected women (n = 49) were evaluated. The overall sexual dysfunction prevalence was 53.7% (65/121), which was higher in the HAM/TSP group (80.0%; adjusted PR 1.89; 95% CI 1.23–2.90) when compared with non-infected individuals (44.9%). Sexual dysfunction was found in 54.4% of the HTLV-1–infected asymptomatic women (PR 1.21; 95% CI 0.82–1.79). Sexual dysfunction was associated with income lower than 1 minimal wage (∼US $300, October 2017) and number of previous birthday.

Conclusion
The obtained results indicate that sexual dysfunction is associated with HAM/TSP in women infected with HTLV-1 of reproductive age.
PIWI genes and piRNAs are ubiquitously expressed in mollusks and show patterns of lineage-specific adaptation
Authors: Jehn Julia , Gebert Daniel , Pipilescu Frank , Stern Sarah , Kiefer Julian Simon Thilo , Hewel Charlotte , Rosenkranz David 
Published: September 2018

AbstractPIWI proteins and PIWI-interacting RNAs (piRNAs) suppress transposon activity in animals, thus protecting their genomes from detrimental insertion mutagenesis. Here, we reveal that PIWI genes and piRNAs are ubiquitously expressed in mollusks, similar to the situation in arthropods. We describe lineage-specific adaptations of transposon composition in piRNA clusters in the great pond snail and the pacific oyster, likely reflecting differential transposon activity in gastropods and bivalves. We further show that different piRNA clusters with unique transposon composition are dynamically expressed during oyster development. Finally, bioinformatics analyses suggest that different populations of piRNAs presumably bound to different PIWI paralogs participate in homotypic and heterotypic ping-pong amplification loops in a tissue- and sex-specific manner. Together with recent findings from other animal species, our results support the idea that somatic piRNA expression represents the ancestral state in metazoans.