bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prediction of folding mechanisms for Ig‐like beta sandwich proteins based on inter‐residue average distance statistics methods
Authors: Aumpuchin Panyavut , Kikuchi Takeshi 
Published: December 2018

AbstractTo understand the folding mechanism of a protein is one of the goals in bioinformatics study. Nowadays, it is enigmatic and difficult to extract folding information from amino acid sequence using standard bioinformatics techniques or even experimental protocols which can be time consuming. To overcome these problems, we aim to extract the initial folding unit for titin protein (Ig and fnIII domains) by means of inter‐residue average distance statistics, Average Distance Map (ADM) and contact frequency analysis (F‐value). TI I27 and TNfn3 domains are used to represent the Ig‐domain and fnIII‐domain, respectively. Beta‐strands 2, 3, 5, and 6 are significant for the initial folding processes of TI I27. The central strands of TNfn3 were predicted as a primary folding segment. Known 3D structure and unknown 3D structure domains were investigated by structure or non‐structure based multiple sequence alignment, respectively, to learn the conserved hydrophobic residues and predicted compact region relevant to evolution. Our results show good correspondence to experimental data, phi‐value and protection factor from H‐D exchange experiments. The significance of conserved hydrophobic residues near F‐value peaks for structural stability using hydrophobic packing is confirmed. Our prediction methods once again could extract a folding mechanism only knowing the amino acid sequence.
AssessingCYP2C19 Ontogeny in Neonates and Infants Using Physiologically Based Pharmacokinetic Models: Impact of Enzyme Maturation Versus Inhibition
Authors: Duan Peng , Wu Fang , Moore Jason N. , Fisher Jeffrey , Crentsil Victor , Gonzalez Daniel , Zhang Lei , Burckart Gilbert J. , Wang Jian 
Published: December 2018

The objective of this study was to develop pediatric physiologically based pharmacokinetic (PBPK) models for pantoprazole and esomeprazole. PediatricPBPKmodels were developed by Simcyp version 15 by incorporating cytochrome P450 (CYP)2C19 maturation and auto‐inhibition. The predicted‐to‐observed pantoprazole clearance (CL) ratio ranged from 0.96–1.35 in children 1–17 years of age and 0.43–0.70 in term infants. The predicted‐to‐observed esomeprazole CL ratio ranged from 1.08–1.50 for children 6–17 years of age, and 0.15–0.33 for infants. The prediction was markedly improved by assuming no auto‐inhibition of esomeprazole in infants in thePBPKmodel. Our results suggested that theCYP2C19 auto‐inhibition model was appropriate for esomeprazole in adults and older children but could not be directly extended to infants. A better understanding of the complex interplay of enzyme maturation, inhibition, and compensatory mechanisms forCYP2C19 is necessary forPBPKmodeling in infants.
Transitions in the wintertime near‐surface temperature inversion at Dome C, Antarctica
Authors: Baas Peter , van de Wiel Bas J. H. , van Meijgaard Erik , Vignon Etienne , Genthon Christophe , van der Linden Steven J. A. , de Roode Stephan R. 
Published: December 2018

In this work we study the dynamics of the surface‐based temperature inversion over the Antarctic Plateau during the polar winter. Using 6 years of observations from the French–Italian Antarctic station Concordia at Dome C, we investigate sudden regime transitions in the strength of the near‐surface temperature inversion. Here we define “near‐surface” as being within the domain of the 45‐m measuring tower. In particular, we consider the strongly nonlinear relation between the 10‐m inversion strength (T10m – Ts) and the 10‐m wind speed.To this end, all individual events for which the 10‐m inversion strength increases or decreases continuously by more than 15 K in time are considered. Composite time series and vertical profiles of wind and temperature reveal specific characteristics of the transition from weak to very strong inversions and vice versa. In contrast to midlatitudes, the largest variations in temperature are not found at the surface but at a height of 10 m.A similar analysis was performed on results from an atmospheric single‐column model (SCM). Overall, the SCM results reproduce the observed characteristics of the transitions in the near‐surface inversion remarkably well. Using model output, the underlying mechanisms of the regime transitions are identified. The nonlinear relation between inversion strength and wind speed at a given level is explained by variations in the geostrophic wind speed, changes in the depth of the turbulent layer and the vertical divergence of turbulent fluxes. Moreover, the transitions between different boundary layer regimes cannot be explained without considering the contribution of subsidence heating.
A Novel Shim-Assisted Resistance Spot Welding Process to Improve Weldability of Medium-Mn Transformation-Induced Plasticity Steel
Authors: Li Shuoshuo , Yang Shanglu , Lu Qi , Luo Haiwen , Tao Wu 
Published: December 2018

Abstract
Medium-Mn transformation-induced plasticity steels have great potential to significantly reduce vehicle weight and improve fuel economy due to their outstanding combination of high strength and excellent ductility. One bottleneck to the application is their poor weldability resulting from their high Mn contents. In this paper, three resistance spot welding set-ups, including no shim, an interstitial-free steel shim at the faying interface (shim-in) and shims against the electrodes (shim-out), were incorporated to investigate the weldability of Fe-7Mn-0.14C medium-Mn steel. Tensile-shear, cross-tension, and microhardness tests were used to evaluate the mechanical properties of the welds. Experimental results demonstrated that the failure mode of the welds transitioned from the interfacial fracture in the case of no shim to the desired nugget pull-out fracture in the shim-out set-up, resulting in dramatical improvements in both peak loads and their corresponding extensions during the tensile-shear and cross-tension tests. In contrast, the shim-in set-up made no improvement. What can contribute to such improvement was then discussed on the basis of observed morphologies and microstructures of welds.
Disembedded Politics: Neoliberal Reform and Labour Market Institutions in Central and Eastern Europe
Authors: Pula Besnik 
Published: December 2018

AbstractDefying predictions of radical liberalization, labour market institutions in post-socialist Central and Eastern Europe are characterized by relatively protective employment legislation, sometimes combined with collective bargaining rights. However, not all protective employment regimes survived political attack by neoliberal reformers. Existing theories in comparative political economy suggest that employment regimes reflect the relative political power of producer groups. Others have suggested that in Central and Eastern Europe the content of labour market reform was determined by the coercive influence of transnational actors. Through a comparative analysis of labour market reform in Bulgaria, Czech Republic, Romania and Slovakia, this article finds that trade unions played a key role in early institutional settlements over labour markets. However, in Romania and Slovakia, these institutional settlements were subsequently undermined by attacks by ideologically motivated domestic elites in episodes of disembedded politics. The article develops the concept of disembedded politics and demonstrates its importance in post-socialist institutional change.
Human factors–based risk analysis to improve the safety of doffing enhanced personal protective equipment
Authors: Gurses Ayse P. , Dietz Aaron S. , Nowakowski Elaine , Andonian Jennifer , Schiffhauer Maggie , Billman Carrie , Abashian Anya M. , Trexler Polly , Osei Patience , Benishek Lauren E. , Xie Anping , Pronovost Peter , Rosen Michael A. , Maragakis Lisa L. ,   for the CDC Prevention Epicenter Program
Published: December 2018

AbstractObjectiveTo systematically assess enhanced personal protective equipment (PPE) doffing safety risks.DesignWe employed a 3-part approach to this study: (1) hierarchical task analysis (HTA) of the PPE doffing process; (2) human factors-informed failure modes and effects analysis (FMEA); and (3) focus group sessions with a convenience sample of infection prevention (IP) subject matter experts.SettingA large academic US hospital with a regional Special Pathogens Treatment Center and enhanced PPE doffing protocol experience.ParticipantsEight IP experts.MethodsThe HTA was conducted jointly by 2 human-factors experts based on the Centers for Disease Control and Prevention PPE guidelines. The findings were used as a guide in 7 focus group sessions with IP experts to assess PPE doffing safety risks. For each HTA task step, IP experts identified failure mode(s), assigned priority risk scores, identified contributing factors and potential consequences, and identified potential risk mitigation strategies. Data were recorded in a tabular format during the sessions.ResultsOf 103 identified failure modes, the highest priority scores were associated with team members moving between clean and contaminated areas, glove removal, apron removal, and self-inspection while preparing to doff. Contributing factors related to the individual (eg, technical/ teamwork competency), task (eg, undetected PPE contamination), tools/technology (eg, PPE design characteristics), environment (eg, inadequate space), and organizational aspects (eg, training) were identified. Participants identified 86 types of risk mitigation strategies targeting the failure modes.ConclusionsDespite detailed guidelines, our study revealed 103 enhanced PPE doffing failure modes. Analysis of the failure modes suggests potential mitigation strategies to decrease self-contamination risk during enhanced PPE doffing.
Lake-level variability in Salar de Coipasa, Bolivia during the past ∼40,000 yr
Authors: Nunnery J. Andrew , Fritz Sherilyn C. , Baker Paul A. , Salenbien Wout 
Published: December 2018

AbstractVarious paleoclimatic records have been used to reconstruct the hydrologic history of the Altiplano, relating this history to past variability of the South American summer monsoon. Prior studies of the southern Altiplano, the location of the world’s largest salt flat, the Salar de Uyuni, and its neighbor, the Salar de Coipasa, generally agree in their reconstructions of the climate history of the past ∼24 ka. Some studies, however, have highly divergent climatic records and interpretations of earlier periods. In this study, lake-level variation was reconstructed from a ∼14-m-long sediment core from the Salar de Coipasa. These sediments span the last ∼40 ka. Lacustrine sediment accumulation was apparently continuous in the basin from ∼40 to 6 ka, with dry or very shallow conditions afterward. The fossil diatom stratigraphy and geochemical data (δ13C, δ15N, %Ca, C/N) indicate fluctuations in lake level from shallow to moderately deep, with the deepest conditions correlative with the Heinrich-1 and Younger Dryas events. The stratigraphy shows a continuous lake of variable depth and salinity during the last glacial maximum and latter stages of Marine Oxygen Isotope Stage 3 and is consistent with environmental inferences and the original chronology of a drill core from Salar de Uyuni.
Variable sialic acid content in milk of Indian cattle and buffalo across different stages of lactation
Authors: Sharma Rekha , Ahlawat Sonika , Sharma Himani , Aggarwal R.A.K. , Sharma Vivek , Tantia M.S. 
Published: December 2018

AbstractThe aim of this Research Communication was to contribute to the knowledge of milk sialic acid concentration of bovines with specific focus on India. Sialic acids (SA) are important constituents of mammalian milks. Buffaloes are the main milk producing species in India, therefore, our research focused on both cow and buffalo. Two Indian cattle (Bos indicus) breeds (Sahiwal, Tharparkar), one cross bred cattle – Karan Fries (Tharparkar × Holstein Friesian) and a buffalo breed (Murrah) were selected. Systematic comparisons of the total, free and bound form of SA and also its distribution over the course of lactation- colostrums and mature milk (120–140 d) was generated. Animal management, sample collection and methodology of SA estimation were identical for the different groups. Colostrum had the highest concentration of SA, which declined with the progress of lactation in all the groups. Majority of the SA existed in bound form. No significant (P < 0.05) difference was recorded in the total, bound or free SA across all the groups. However, differences were obvious in the total and bound SA level in the mature milk. Indian cattle, Sahiwal and Tharparkar were equivalent, but had higher concentration of total and bound SA than crossbred cattle. Milk of buffalo had SA equivalent to that of crossbred cattle. The mean (se) levels of total SA was 23.4 (0.8), 25.8 (2.4), 20.3 (0.6) and 20.2 (1.2) in Sahiwal, Tharparkar, cross bred and Murrah buffalo, respectively. The findings suggested that milk of indigenous cattle may be a potential source of SA, a bioactive compound with beneficial effect on human health and a potential functional ingredient in foods. Results add value to the currently declining indigenous cattle of India.
An amended description of two Gyrodactylus species (Platyhelminthes: Monogenea) parasitizing Antarctic Notothenioid fish
Authors: Heglasová I. , Nezhybová V. , Přikrylová I. 
Published: December 2018

Abstract
Species identification based on the morphometry of opisthaptoral hard parts, in combination with internal transcribed spacer ribosomal DNA (ITS rDNA) region sequences, confirmed the presence of four viviparous Gyrodactylus von Nordman, 1832 (Plathyhelminthes, Monogenea) species on Nototheniid fish from the Prince Gustav Channel (Weddell Sea, Antarctica). Gyrodactylus antarcticus Gusev, 1967 was found mostly on Trematomus newnesi Boulenger (93 specimens) but also on T. bernacchii Boulenger (one specimen), the latter representing a new host record for this species. Gyrodactylus byrdi Hargis & Dillon, 1968 and G. coriicepsi Rokicka, Lumme & Ziętara, 2009 were recorded on their type hosts, T. newnesi and Notothenia coriiceps Richardson, respectively. Gyrodactylus wilkesi Hargis & Dillon, 1968 was found mostly on the fins of T. bernacchii (29 specimens), but also on T. hansoni Boulenger (one specimen) and T. newnesi (three specimens). The finding of G. wilkesi on T. newnesi represents a new host record. The low number of Gyrodactylus specimens may indicate an accidental infection. The occurence of all four Gyrodactylus species in the Prince Gustav Channel represents a new locality record. According to phylogentic methods, the newly redescribed monogeneans belong to the Antarctic lineage, forming a sister group to North American and European marine Gyrodactylus species, and consist of two species groups, one comprising G. coriicepsi and G. nudifronsi Rokicka, Lumme & Ziętara, 2009, and the other G. anarcticus and G. wilkesi.
A re-evaluation of thelotremoidGraphidaceae(lichenized Ascomycota:Ostropales) in India
Authors: JOSHI Santosh , UPRETI Dalip K. , DIVAKAR Pradeep K. , LUMBSCH H. Thorsten , LÜCKING Robert 
Published: December 2018

AbstractAn account of thelotremoid species ofGraphidaceaein India is provided, which includes 124 species in 24 genera.OcellulariaandThelotremaare the most diverse genera represented by 34 and 18 species, respectively. Type specimens were re-examined and additional samples studied morphologically and chemically. One new species,Ocellularia upretiiS. Joshi, Divakar, Lumbsch & Lücking, is described; it is characterized by a greyish green thallus, porinoid ascomata, brown proper exciple, simple, carbonized columella, clear hymenium, transversely septate, amyloid ascospores of 110–125×15–20 µm and an absence of secondary metabolites.Asteristion australianum,Astrochapsa mirabilis,Cruentotrema cruentatum,C. kurandense,Ocellularia violaceaandThelotrema adjectumare reported as new to the country, andAstrochapsa mirabilis,Melanotrema submicrosporoides,Ocellularia annuloelevata,O. subkeralensisandRhabdodiscus verrucoisidiatusare proposed as new combinations.Diploschistes awasthii,Ocellularia gupeti,O. leucina, O. mahabalei,Thelotrema confertumandT. verrucorugosumare synonymized underD. scruposus,O. neomasonhalei,O. urceolaris,O. thelotremoides,Chapsa leprocarpoidesandT. rugatulum, respectively, withOcellularia canarianaandO. verrucomarginatareduced to synonymy withO. allosporoides.
The Effect of a Mainshock on the Size Distribution of the Aftershocks
Authors: Gulia L. , Rinaldi A. P. , Tormann T. , Vannucci G. , Enescu B. , Wiemer S. 
Published: December 2018

AbstractA systematic decay of the aftershock rate over time is one of the most fundamental empirical laws in Earth science. However, the equally fundamental effect of a mainshock on the size distribution of subsequent earthquakes has still not been quantified today and is therefore not used in earthquake hazard assessment. We apply a stacking approach to well‐recorded earthquake sequences to extract this effect. Immediately after a mainshock, the mean size distribution of events, orbvalue, increases by 20–30%, considerably decreasing the chance of subsequent larger events. This increase is strongest in the immediate vicinity of the mainshock, decreasing rapidly with distance but only gradually over time. We present a model that explains these observations as a consequence of the stress changes in the surrounding area caused by the mainshocks slip. Our results have substantial implications for how seismic risk during earthquake sequences is assessed.
Floe Size Effect on Gravity Wave Propagation Through Ice Covers
Authors: Cheng Sukun , Tsarau Andrei , Evers Karl‐Ulrich , Shen Hayley 
Published: December 2018

AbstractWhen modeling gravity wave propagation through an array of discrete ice floes, considered as a homogenous elastic continuum, the equivalent elasticity is less than the intrinsic material elasticity of ice. The array behaves increasingly like a collection of rigid floating masses when the floe sizes decrease. Extending a former wave flume experiment with polyethylene plates (Sakai & Hanai, 2002, https://web2.clarkson.edu/projects/iahrice/IAHR%202002/Volume%202/189.pdf), we conducted an experiment with saline ice floes at the Hamburg Ship Model Basin (HSVA). Using the measured wave number and the dispersion relation from a continuous elastic plate theory, we determine the equivalent elasticity. Parallel theoretical solutions are obtained using the matched eigenfunction expansion method (Kohout et al., 2007, https://doi.org/10.1016/j.jfluidstructs.2006.10.012), assuming ice floes as an array of thin elastic plates floating over inviscid water. Despite data scatter in laboratory tests, the celerity (phase speed) from the laboratory and theoretical results both show a decreasing trend when the floe size reduces. The corresponding equivalent elastic modulus decreases from the intrinsic modulus to zero. The matched eigenfunction expansion method is then applied to investigate cases under field conditions. Using all the theoretical results, an empirical relation is proposed for the equivalent elasticity in terms of wavelength, floe size, and length scale from the intrinsic elasticity of the floes. In addition to celerity, wave amplitude along the ice cover is compared with the theoretical results. Large discrepancies of wave attenuation from laboratory and theoretical solutions are found, indicating that attenuation mechanisms other than wave scattering need to be considered.
Accurate Laboratory Measurement of the O2 Collision‐Induced Absorption Band Near 1.27 μm
Authors: Mondelain D. , Kassi S. , Campargue A. 
Published: December 2018

AbstractThe atmospheric band of O2 near 1.27 μm plays an important role in determining the air mass from ground or spaceborne atmospheric spectra. This band consists of narrow absorption lines of the
transitions superimposed to a much broader collision‐induced absorption (CIA) structure. Very accurate CIA binary coefficients,
,
, and
, are determined by highly sensitive cavity ring down spectroscopy from low density spectra (0.36 to 0.85 amagat) of pure oxygen and an O2/N2 mixture (20.96%/79.04%) at room temperature over the 7,513–8,466‐cm−1 region. Two cavity ring down spectrometers involving 12 distributed feedback lasers and two external cavity diode lasers were used below and above 7,920 cm−1, respectively. The measurements performed at different densities show a percent level consistency. This accuracy results from (i) a high baseline stability of the spectra, (ii) an accurate determination of the baseline using argon spectra recorded for the same densities, and (iii) a reliable removal of the local contribution of the absorption lines made easier thanks to subatmospheric pressure recordings. The retrieved binary coefficients are compared to the experimental data included in HITRAN2016 database (Maté et al., 1999, https://doi.org/10.1029/1999JD900824), to the dataset used for Total Carbon Column Observing Network spectra as well as to recent ab initio calculations. Although more accurate, the binary coefficients reported here are found in agreement with the Maté et al. measurements using high pressure Fourier transform spectroscopy. The derived value of the integrated CIA band intensity
= 1.31(3) × 10−4 cm−2 amagat−2 exceeds the corresponding Fourier transform spectroscopy value by about 3%.
Global Pyrogenic Carbon Production During Recent Decades Has Created the Potential for a Large, Long‐Term Sink of Atmospheric CO2
Authors: Wei Xinyuan , Hayes Daniel J. , Fraver Shawn , Chen Guangsheng 
Published: December 2018

AbstractFires play an important role in the terrestrial biosphere carbon cycle, not only through direct carbon release but also contributing to a potential long‐term storage as pyrogenic carbon (PyC). PyC is formed through fires, and, because it may resist further biological and chemical degradation, is more stable in soil and sediment than original biomass. At the global scale, contributions of fires to both atmospheric CO2emissions and PyC accumulation are potentially large but difficult to estimate. Our analysis was based on existing simulation results from two different modeling approaches (Global Fire Emissions Database version 4 [GFED4s] and Terrestrial Ecosystem Model version 6 [TEM6]) that used global area burned data to provide recent, retrospective estimates of CO2emissions from vegetation combustion, together with published, biome‐ and continental‐scale conversion ratios that relate CO2emissions to PyC production (PyC/CO2) during combustion. The estimates of global CO2emissions from fires differed substantially between the two models' results. GFED4s estimated 2,041 Tg C/year during the 2000–2016 time period, whereas the TEM6 estimate was considerably lower at 643 Tg C/year from 2000 to 2010. Global PyC production estimates from fires were 153.4 ± 18.7 and 49.5 ± 4.9 Tg C/year based on the emission estimates from GFED4s and TEM6, respectively. Our results suggest that African tropical savanna fires produced the largest amount of CO2emissions and PyC among global biomes, the most significant interannual variations in CO2emissions and PyC production were found in tropical forests, and the magnitude of PyC produced by fires each year represented a potentially significant long‐term sink of atmospheric CO2.