bluuebunny/crossref_metadata_2025_split huggingface dataset:
Roadmap for an early gene therapy for cystic fibrosis airway disease
Authors: Carlon Marianne S. , Vidović Dragana , Birket Susan 
Published: October 2017

AbstractGene therapy provides a mutation‐independent approach to treat or even cure CF airway disease. To develop a clinical candidate for CF gene therapy, a thorough examination of preclinical efficacy in relevant cell and animal models is a prerequisite. For a long time, the CF field was struggling with a lack of appropriate animal models for CF airway pathology. Since 2008, many different and complementary animal models have been generated that develop hallmarks of CF airway disease, including the CF pig, ferret, and rat. With this, a new era has arisen that allows investigating the efficacy of gene therapy beyond molecular and electrophysiological end‐points. Successful gene therapy most likely requires an appropriate time window. CF lung pathology progresses with age and therefore an early treatment would be beneficial to prevent irreversible damage. In that regard, newborn screening programs and prenatal diagnosis already provide a basis to facilitate future preventive gene‐based treatment. If successful, gene therapy for CF airway disease would markedly reduce the treatment burden and improve life quality and life expectancy of CF patients.
Proteome and Structural Organization of the Knob Complex on the Surface of the Plasmodium Infected Red Blood Cell
Authors: Alampalli Shuba Varshini , Grover Manish , Chandran Syama , Tatu Utpal , Acharya Pragyan 
Published: October 2017

PurposeThe cell membrane of the erythrocytes infected with the malaria parasite Plasmodium falciparum undergoes several changes during the course of parasite life cycle and forms protrusions known as ‘knobs’ on its surface during the mature trophozoite and schizont stages. The structural organization of knob components especially PfEMP1 on the iRBC surface is the main determinant for the cytoadhesive and rosetting capacity of the iRBC by binding to various host receptors as well as for the variable antigenicity, which is crucial for immunoevasion. Although several studies report individual interactions among knob constituents, a comprehensive identification of the knob proteome is lacking.Experimental designThe detergent‐resistant membrane (DRM) rafts are isolated from the infected erythrocyte membrane and knob (KAHRP) positive fractions are subjected to proteomics analysis. In addition, structures of various knob components are modeled and assembled ab initio based on experimentally established protein interactions.ResultsProteins of various functional classes are found to be present in the knobs including the newly identified knob constituents which include host Hsp70, elongation factor 1A, acyl CoA synthetase, and some hypothetical proteins. Ab initio structural prediction of PfEMP1, KHARP, PfEMP2, PfEMP3, and PHIST shows that these proteins are intrinsically disordered and can have varying number of protein–protein interactions depending on their lowest energy structure. Further in silico mathematical modeling of a single repeat unit of PfEMP1–PHIST is present 63–112 times along the periphery of a single knob.Conclusions and clinical relevanceThis study provides structural insight into the organization of the core knob components and uncovers novel proteins as knob components. This structural information can be used for the development of better vaccine design strategies or drug design to destabilize the knob structure, which is a major virulence determinant in P. falciparum malaria.
PepSweetener: A Web‐Based Tool to Support Manual Annotation of Intact Glycopeptide MS Spectra
Authors: Domagalski Marcin Jakub , Alocci Davide , Almeida Andreia , Kolarich Daniel , Lisacek Frédérique 
Published: October 2017

PurposePepSweetener is a web‐based visualization tool designed to facilitate the manual annotation of intact glycopeptides from MS data regardless of the instrument that produced these data.Experimental designThis exploratory tool uses a theoretical glycopeptide dataset to visualize all peptide‐glycan combinations that fall within the error range of the query precursor ion. PepSweetener simplifies the determination of the correct peptide and glycan composition of a glycopeptide based on its precursor mass. The theoretical glycopeptide search space can be customized in an advanced query mode that specifies potential proteins/peptides, glycan compositions, and several experimental parameters.ResultsPepSweetener displays the results on an interactive heat‐map chart where theoretical glycopeptide tile colors correspond to ppm deviations from the query precursor mass. Additionally, a visualization chart incorporates glycan composition filtering, sorting by mass and tolerance, and an in silico peptide fragmentation diagram is provided to further support the correct glycopeptide identification.Conclusions and clinical relevancePepSweetener efficiently allows the selection of the most probable intact glycopeptide mass matches and speeds up the verification process. It is validated on serum protein samples and immunoglobulins. The tool is publicly hosted on ExPASy, the SIB Swiss Institute of Bioinformatics resource portal (http://glycoproteome.expasy.org/pepsweetener/app/).
A Review of Illuminating Pyrotechnics
Authors: Sabatini Jesse J. 
Published: October 2017

AbstractThis review article consists of efforts focused on the development of illuminating pyrotechnics. Examined will be the methods of generating red‐, green‐, yellow‐ and blue‐light‐emitting illuminating pyrotechnics. Ways to improve luminosity, spectral purity, and burn rate will be discussed. Recently developed formulations concerning the development of environmentally friendly illuminating pyrotechnics will also be presented.
Moisture transport by tropical plumes over the Middle East: a 30‐year climatology
Authors: Tubi Amit , Dayan Uri , Lensky Itamar M. 
Published: October 2017

This study conducts a 30‐year climatological analysis of tropical plumes (TPs) observed over the Middle East (ME). These moisture bursts, conveying water vapour from tropical Africa to the arid ME at mid‐ to upper tropospheric levels, were identified and analysed using multiple data sources and empirical tools, including satellite images, reanalysis data, backward trajectories, and calculation of moisture profiles, water vapour transport and moisture flux convergence. The analysis of the 140 days in which TPs were identified focused on three main elements: (i) TP seasonal distribution and contribution to rainfall regime, (ii) TP moisture pathways, and (iii) the mechanisms leading to TP‐induced precipitation.TPs over the ME are found to be most frequent in the winter season, with the second highest frequency observed during the spring. The estimation of TPs' contribution to the rainfall regime over the ME, the first of its kind, shows that such contribution is limited. However, extreme events may have a significant effect on the overall annual precipitation amount.Two moisture pathways are identified, exhibiting very limited mixing, if any, with the dry air mass at shallow tropospheric levels. The first, originating in tropical West Africa, is associated with the penetration of an intensified subtropical jet stream towards lower latitudes. The second, emanating from East to Central African sources, is closely associated with an anomalous anticyclonic flow over southern Arabia. Moisture conveyed by the latter pathway is supplied from sources that are closer to the target area, transported at lower atmospheric levels, and exhibits more pronounced vertical dispersion.Compared to TPs that did not lead to precipitation, precipitative TPs feature enhanced moisture transport and stronger convergence of moisture flux. Similarly, the belt of moisture flux convergence stretching from the Tropics to the ME is interrupted when non‐precipitative TPs occur but uninterrupted during precipitative events.
Impaired caudal fin‐fold regeneration in zebrafish deficient for the tumor suppressor Pten
Authors: Hale Alexander James , Kiai Ali , Sikkens Jelte , den Hertog Jeroen 
Published: October 2017

AbstractZebrafish are able to completely regrow their caudal fin‐folds after amputation. Following injury, wound healing occurs, followed by the formation of a blastema, which produces cells to replace the lost tissue in the final phase of regenerative outgrowth. Here we show that, surprisingly, the phosphatase and tumor suppressor Pten, an antagonist of phosphoinositide‐3‐kinase (PI3K) signaling, is required for zebrafish caudal fin‐fold regeneration. We found that homozygous knock‐out mutant (ptena−/−ptenb−/−) zebrafish embryos, lacking functional Pten, did not regenerate their caudal fin‐folds. AKT phosphorylation was enhanced, which is consistent with the function of Pten. Reexpression of Pten, but not catalytically inactive mutant Pten‐C124S, rescued regeneration, as did pharmacological inhibition of PI3K. Blastema formation, determined by in situ hybridization for the blastema marker junbb, appeared normal upon caudal fin‐fold amputation of ptena−/−ptenb−/− zebrafish embryos. Whole‐mount immunohistochemistry using specific markers indicated that proliferation was arrested in embryos lacking functional Pten, and that apoptosis was enhanced. Together, these results suggest a critical role for Pten by limiting PI3K signaling during the regenerative outgrowth phase of zebrafish caudal fin‐fold regeneration.
Tailoring N‐Terminated Defective Edges of Porous Boron Nitride for Enhanced Aerobic Catalysis
Authors: Wu Peiwen , Yang Shize , Zhu Wenshuai , Li Hongping , Chao Yanhong , Zhu Huiyuan , Li Huaming , Dai Sheng 
Published: October 2017

AbstractTailoring terminated edge of hexagonal boron nitride (h‐BN) for enhancing catalysis has turned to be an imperative for the rational design of a highly active aerobic catalyst. Herein, a tailoring N‐terminated porous BN (P‐BN) strategy is reported with a zinc (Zn) salt as a dual‐functional template. The Zn salt acts as both an in situ template and an N‐terminated defective edges directing agent. The zinc salt template turns to Zn nanoparticles (Zn NPs) and functions as physical spacers, which are subsequently removed at a higher temperature, for producing P‐BN, whose high surface area is high to 1579 m2 g−1. Moreover, because of the lower electronegativity of Zn, boron (B) atoms are partly replaced by Zn atoms and ultimately preferred to N‐terminated edges with the volatilization of Zn NPs. Owing to the moderate dissociative energy of oxygen atoms on N‐terminated edges, the N‐terminated edges are proved to be the origin of an enhanced aerobic catalytic activity by density functional theory (DFT) calculations. Moreover, the DFT calculation result is experimentally verified.
Pilot study of MRI/ultrasound fusion imaging in postpartum assessment of Cesarean section scar
Authors: Bolten K. , Fischer T. , Bender Y. Y.‐N. , Diederichs G. , Thomas A. 
Published: October 2017

ABSTRACTObjectiveTo evaluate prospectively the uterine scar after Cesarean section (CS) and the corresponding uterine region after vaginal delivery (VD) at 6 weeks postpartum using transabdominal (TAS) and transvaginal (TVS) sonography with magnetic resonance imaging (MRI) fusion to investigate whether fusion imaging allows standardized and reproducible identification of the scar location and measurement of uterine wall thickness compared with high‐resolution MRI alone.MethodsPelvic MRI was performed 6 weeks after delivery in 30 women (10 with planned CS (PCS), 10 with emergency CS (ECS) and 10 with VD). After transfer of MRI‐DICOM datasets to the ultrasound system, the scar region after CS and the corresponding uterine region after VD were examined by TAS (5 MHz) and TVS (10 MHz) using smart fusion with MRI to guide visualization of the region in the corresponding sectional planes for both modalities. Vascularization of the scar region was determined as a percentage area using power Doppler ultrasound. Anterior (AW) and posterior (PW) uterine wall thickness was measured using TAS and TVS with fusion imaging and using MRI alone.ResultsTVS with fusion imaging was applied successfully for uterine assessment at the end of the postpartum period in all women. TAS failed to identify the scar area in three women. Imaging techniques were similar in the evaluation of AW and PW thickness following VD. MRI and MRI/TVS fusion showed significant differences in AW thickness or scar area, in terms of the difference relative to PW thickness, in women with PCS and ECS (MRI: PCS, 4.3 mm; ECS, 4.2 mm; VD, 0.8 mm; P = 0.034; MRI/TVS fusion: PCS, 2.0 mm; ECS, 3.3 mm; VD, 0.0 mm; P = 0.01). The degree of vascularization in the scar region measured by power Doppler ultrasound was lower after PCS (13.1 ± 9.4%/area) and ECS (17.0 ± 8.2%/area) than after VD (34.6 ± 8.5%/area; P = 0.0017).ConclusionMRI/ultrasound fusion imaging can be performed in a reproducible manner for examination of the postpartum uterus. MRI/TVS fusion enables standardized identification of the CS scar location and vascularization is reduced in this area. Copyright © 2016 ISUOG. Published by John Wiley & Sons Ltd.
Generation of UHV with Turbomolecular Pump and Dry Backing Pump
Authors: Schopphoff Andreas , Braunschweig Falk 
Published: October 2017

SummaryFor the generation of ultra‐high vacuum (UHV), multiple pumps and pump combinations are possible. In the past, due to its high compression ratio, the most commonly used backing pump was the oil‐sealed rotary vane pump. But the growing demand for hydrocarbon‐free vacuum makes other solutions necessary: A completely magnetically levitated turbomolecular pump combined with a dry multistage Roots pump is not only able to generate oil‐free UHV pressure but also eliminates contamination due to operating error. Residual gas analyses prove that with this pump combination, the limiting partial pressure of hydrogen can be significantly reduced.
Combinatorial Magnetron Sputtering
Authors: Gaines J. R. 
Published: October 2017

SummaryCombinatorial Magnetron Sputtering is a process where large numbers of chemically distinct thin film samples can be made in a single deposition. Utilizing a multiple cathode sputter system manufactured by the Kurt J. Lesker Company, researchers at the California Institute of Technology have developed a process which enables them to make 5,000 unique compositions on one 4″ wafer in one deposition. Compositional control is achieved by varying the tilt angle of the cathodes and Z‐distance relative to the substrate. In addition to this extraordinary fabrication capability, the group also developed a model which can predict the range of future compositions as well as a rapid characterization technique which can sort through thousands of compositions in a 24 hour period.
On the Time-Temperature-Transformation Behavior of a New Dual-Superlattice Nickel-Based Superalloy
Authors: Mignanelli P. M. , Jones N. G. , Hardy M. C. , Stone H. J. 
Published: October 2017

Abstract
Recent research has identified compositions of nickel-based superalloys with microstructures containing appreciable and comparable volume fractions of γ′ and γ″ precipitates. In this work, an alloy capable of forming such a dual-superlattice microstructure was subjected to a range of thermal exposures between 873 K and 1173 K (600 °C and 900 °C) for durations of 1 to 1000 hours. The microstructures and nature of the precipitating phases were characterized using synchrotron X-ray diffraction and electron microscopy. These data have enabled the construction of a T-T-T diagram for the precipitating phases. Hardness measurements following each thermal exposure have identified the age-hardening behavior of this alloy and allowed preliminary mechanical properties to be assessed.
Mechanism of Phospholipid Hydrolysis for Oyster Crassostrea plicatula Phospholipids During Storage Using Shotgun Lipidomics
Authors: Chen Qinsheng , Wang Xincen , Cong Peixu , Liu Yanjun , Wang Yuming , Xu Jie , Xue Changhu 
Published: October 2017

AbstractA fast and efficient shotgun lipidomics strategy was applied to analyze phospholipids (PL) in the oyster Crassostrea plicatula, including 29 species of phosphatidylcholine (PtdCho), 23 species of phosphatidylethanolamine (PtdEtn), 11 species of phosphatidylserine (PtdSer), 6 species of phosphatidylinositol (PtdIns), and 17 species of lysophospholipids (Lyso‐PL). During storage at 4 °C for 7 days, the PL content decreased by 68.08%, but a significant increase in the FFA content was observed (from 63.11 to 318.72 μg/g). PtdCho and PtdIns decreased relatively by 64.97 and 67.49%, and PtdSer decreased most markedly by 74.15%. However, the PtdEtn content increased slightly during the early stages of storage but subsequently began to decrease. Moreover, PL with eicosapentaenoic acid (EPA‐PL) and docosahexaenoic acid (DHA‐PL) decreased by 51.77 and 50.61%, whereas plasmalogens were relatively stable showing only a 25.46% decrease. In particular, through enzyme activity analysis of lipase, phospholipase A1 (PLA1), phospholipase A2 (PLA2), phospholipase C (PLC), and phospholipase D (PLD), it was observed that the activities of all these enzymes increased at the early stage at 4 °C, but their activities were at lower levels when the oysters were stored at −20 °C. During the storage period at 4 °C, correlation analysis suggests that the degradation of PtdCho was mostly correlated to PLA2 (p < 0.05), whereas PtdEtn and PtdSer were more markedly correlated to lipase and PLD, respectively. The above result indicates that the hydrolysis mechanism of PL during seafood storage was correlated to the lipid hydrolytic enzyme activities under different storage temperatures.
Transient and limit cycle combustion dynamics analysis of turbulent premixed swirling flames
Authors: Palies Paul , Ilak Milos , Cheng Robert 
Published: October 2017

Premixed low swirling flames (methane–air and hydrogen–methane–air) are experimentally investigated for three different regimes. Stable, local transient to instability and limit cycle regimes corresponding to three distinct equivalence ratios are considered. Dynamic mode decomposition is applied to the hydrogen–air–methane flame to retrieve the modes frequencies, growth rates and spatial distributions for each regime. The results indicate that a vortical wave propagating along the flame front is associated with the transition from stability to instability. In addition, it is shown that a key effect on stability is the location of the non-oscillating (0 Hz) flame component. The phase-averaged unsteady motion of the flames over one cycle of oscillation shows the vortical wave rolling up the flame front. The Rayleigh index maps are formed to identify the region of driving and damping of the self-sustained oscillation, while the flame transfer function phase leads to the propagation mode of the perturbations along the flame front. The second mechanism identified concerns the swirl number fluctuation induced by the mode conversion. By utilizing hypotheses for the flow field and the flame structure, it is pointed out that those mechanisms are at work for both flames (methane–air and hydrogen–methane–air) and their effects on the unsteady heat release are determined. Both unsteady heat release contributions, the vortical wave induces flame surface fluctuations and swirl number oscillation induces unsteady turbulent burning velocity, are in phase opposition and of similar amplitudes.
Formation and development of supraglacial lakes in the percolation zone of the Greenland ice sheet
Authors: CHEN CHRISTINE , HOWAT IAN M. , DE LA PEÑA SANTIAGO 
Published: October 2017

AbstractWe examine repeat surface altimetry and radio echo observations of two supraglacial lakes in the percolation zone of the Greenland ice sheet to investigate the changes in firn conditions leading to lake formation and implications for meltwater storage within firn. Both lakes formed in 2011, when an anomalously high melt season was followed by low winter accumulation, resulting in reduced infiltration and storage in the near surface. The lakes expanded during the 2012 record melt season and retained liquid meltwater through the following winter. The lakes then contracted, with one lake slowly draining and refreezing and another rapidly draining to the subsurface. The lack of observable change in firn conditions surrounding the lakes indicates increased run-off in the near surface firn, likely along low-permeability ice layers formed during the previous melt seasons. This implies a reduced ability of the firn to absorb increased meltwater.
Occurrence ofMicrodictyonfrom the lower Cambrian Xinji Formation along the southern margin of the North China Platform
Authors: Pan Bing , Topper Timothy P. , Skovsted Christian B. , Miao Lanyun , Li Guoxiang 
Published: October 2017

AbstractDisarticulated net-like plates of the lobopodMicrodictyonhad a near cosmopolitan distribution from the early to middle Cambrian but are yet to be documented from the North China Platform. Here we report isolated plates ofMicrodictyonfrom the lower Cambrian Xinji Formation (Stage 4, Series 2) of the North China Platform, extending the paleogeographic distribution ofMicrodictyonin the early Cambrian. The plates ofMicrodictyonfrom the Xinji Formation are similar to those of other species established on the basis of isolated plates but do bear some new characters, such as mushroom-shaped nodes with a single inclined platform-like apex and an upper surface that displays radial lines. However, the plates documented here are left under open nomenclature due to inadequate knowledge of intraspecific and ontogenetic variation and low specimen numbers. Through comparison of the node shapes of the isolated plates of differentMicrodictyonspecies, we consider that low mushroom-shaped nodes could be a primitive and conservative character ofMicrodictyonwhile tall mushroom-shaped nodes may be a derived character. Subtle differences in shape and number of node apices may also represent intraspecific or ontogenetic variation.
Law PORT: an Online Training Initiative to Improve the Legal Information Skills of Postgraduate Researchers
Authors: Davies Lisa 
Published: October 2017

AbstractIn this article Lisa Davies, Access Librarian at the Institute of Advanced Legal Studies, reports on a recent initiative to create online tutorials to improve the legal information skills of postgraduate researchers. She describes the aims of the project, outlines the steps that were taken to create the new training resources, details the content of the tutorials, looks back on the main challenges faced and considers plans for the future.
Algorithms and the Rule of Law
Authors: Kennedy Rónán 
Published: October 2017

AbstractIn this short article Rónán Kennedy explores fundamental issues surrounding the use of algorithms in the context of the rule of law in our society. He states, ‘The issues that are buried in these systems should be a matter of serious concern for law and lawyers as we try to protect fundamental values in the 21st century, and we try to properly represent our clients’ interests against systems errors that we cannot easily identify’.*