bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural insight for the roles of fas death domain binding to fadd and oligomerization degree of the fas–fadd complex in the death‐inducing signaling complex formation: A computational study
Authors: Yan Qi , McDonald Jay M. , Zhou Tong , Song Yuhua 
Published: January 2013

AbstractFas binding to Fas‐associated death domain (FADD) activates FADD–caspase‐8 binding to form death‐inducing signaling complex (DISC) that triggers apoptosis. The Fas–Fas association exists primarily as dimer in the Fas–FADD complex, and the Fas–FADD tetramer complexes have the tendency to form higher order oligomer. The importance of the oligomerized Fas–FADD complex in DISC formation has been confirmed. This study sought to provide structural insight for the roles of Fas death domain (Fas DD) binding to FADD and the oligomerization of Fas DD–FADD complex in activating FADD–procaspase‐8 binding. Results show Fas DD binding to FADD stabilized the FADD conformation, including the increased stability of the critical residues in FADD death effector domain (FADD DED) for FADD–procaspase‐8 binding. Fas DD binding to FADD resulted in the decreased degree of both correlated and anticorrelated motion of the residues in FADD and caused the reversed correlated motion between FADD DED and FADD death domain (FADD DD). The exposure of procaspase‐8 binding residues in FADD that allows FADD to interact with procaspase‐8 was observed with Fas DD binding to FADD. We also observed different degrees of conformational and motion changes of FADD in the Fas DD–FADD complex with different degrees of oligomerization. The increased conformational stability and the decreased degree of correlated motion of the residues in FADD in Fas DD–FADD tetramer complex were observed compared to those in Fas DD–FADD dimer complex. This study provides structural evidence for the roles of Fas DD binding to FADD and the oligomerization degree of Fas DD–FADD complex in DISC formation to signal apoptosis. Proteins 2013. © 2012 Wiley Periodicals, Inc.
Structure refinement of protein model decoys requires accurate side‐chain placement
Authors: Olson Mark A. , Lee Michael S. 
Published: January 2013

AbstractIn this study, the application of temperature‐based replica‐exchange (T‐ReX) simulations for structure refinement of decoys taken from the I‐TASSER dataset was examined. A set of eight nonredundant proteins was investigated using self‐guided Langevin dynamics (SGLD) with a generalized Born implicit solvent model to sample conformational space. For two of the protein test cases, a comparison of the SGLD/T‐ReX method with that of a hybrid explicit/implicit solvent molecular dynamics T‐ReX simulation model is provided. Additionally, the effect of side‐chain placement among the starting decoy structures, using alternative rotamer conformations taken from the SCWRL4 modeling program, was investigated. The simulation results showed that, despite having near‐native backbone conformations among the starting decoys, the determinant of their refinement is side‐chain packing to a level that satisfies a minimum threshold of native contacts to allow efficient excursions toward the downhill refinement regime on the energy landscape. By repacking using SCWRL4 and by applying the RWplus statistical potential for structure identification, the SGLD/T‐ReX simulations achieved refinement to an average of 38% increase in the number of native contacts relative to the original I‐TASSER decoy sets and a 25% reduction in values of Cα root‐mean‐square deviation. The hybrid model succeeded in obtaining a sharper funnel to low‐energy states for a modeled target than the implicit solvent SGLD model; yet, structure identification remained roughly the same. Without meeting a threshold of near‐native packing of side chains, the T‐ReX simulations degrade the accuracy of the decoys, and subsequently, refinement becomes tantamount to the protein folding problem. Proteins 2013. 2012 Published by Wiley Periodicals, Inc.
Starting‐structure dependence of nanosecond timescale intersubstate transitions and reproducibility of MD‐derived order parameters
Authors: Zeiske Tim , Stafford Kate A. , Friesner Richard A. , Palmer Arthur G. 
Published: January 2013

AbstractFactors affecting the accuracy of molecular dynamics (MD) simulations are investigated by comparing generalized order parameters for backbone NH vectors of the B3 immunoglobulin‐binding domain of streptococcal protein G (GB3) derived from simulations with values obtained from NMR spin relaxation (Yao L, Grishaev A, Cornilescu G, Bax A, J Am Chem Soc 2010;132:4295‐4309.). Choices for many parameters of the simulations, such as buffer volume, water model, or salt concentration, have only minor influences on the resulting order parameters. In contrast, seemingly minor conformational differences in starting structures, such as orientations of sidechain hydroxyl groups, resulting from applying different protonation algorithms to the same structure, have major effects on backbone dynamics. Some, but not all, of these effects are mitigated by increased sampling in simulations. Most discrepancies between simulated and experimental results occur for residues located at the ends of secondary structures and involve large amplitude nanosecond timescale transitions between distinct conformational substates. These transitions result in autocorrelation functions for bond vector reorientation that do not converge when calculated over individual simulation blocks, typically of length similar to the overall rotational diffusion time. A test for convergence before averaging the order parameters from different blocks results in better agreement between order parameters calculated from different sets of simulations and with NMR‐derived order parameters. Thus, MD‐derived order parameters are more strongly affected by transitions between conformational substates than by fluctuations within individual substates themselves, while conformational differences in the starting structures affect the frequency and scale of such transitions. Proteins 2013. © 2012 Wiley Periodicals, Inc.
Validation of the forecast skill of the Global Modeling and Assimilation Office Observing System Simulation Experiment
Authors: Privé N. C. , Errico R. M. , Tai K.‐S. 
Published: January 2013

AbstractA global Observing System Simulation Experiment (OSSE) framework has been developed at the National Aeronautics and Space Administration Global Modeling and Assimilation Office (NASA/GMAO). The OSSE uses a 13‐month integration of the European Centre for Medium‐Range Weather Forecasts (ECMWF) operational model as the Nature Run, and the Goddard Earth Observing System version‐5 (GEOS‐5) forecast model with Gridpoint Statistical Interpolation (GSI) data assimilation as the forecast model. Synthetic observations have been developed with correlated observation errors to replicate the observing network from 2005–2006.The performance of the GMAO OSSE in terms of forecast skill and observation impacts is evaluated against real observational data for the same period. Metrics of anomaly correlation of 500 hPa geopotential and root‐mean‐square error of temperature and wind fields for 120 h forecasts are calculated for once‐daily forecasts from July 2005, and an adjoint is used to measure observation impacts of different data types. The forecast skill of the OSSE is found to be slightly higher than for real data, with smaller observation impacts overall, possibly due to insufficient model error in the OSSE. While there is similar relative ranking of observation impact for most data types in the OSSE compared with real data, for individual satellite channels the agreement is not as good. Some caveats and difficulties of using the OSSE system are discussed along with recommendations of how to avoid potential pitfalls when performing OSSEs.
A storm surge inundation model of the northern Bay of Bengal using publicly available data
Authors: Lewis Matt , Bates Paul , Horsburgh Kevin , Neal Jeff , Schumann Guy 
Published: January 2013

AbstractA computationally inexpensive inundation model has been developed from freely available data sources for the northern Bay of Bengal region to estimate flood risk from storm surges. This is the first time Shuttle Radar Topography Mission (SRTM) terrain data have been used in a dynamic coastal inundation model. To reduce SRTM noise, and the impact of vegetation artefacts on the ground elevation, the SRTM data were up‐scaled from their native 90 m resolution to 900 m. A sub‐grid routine allowed estuary channels with widths less than this resolution to be simulated efficiently, and allowed six major river flows to be represented. The inundation model was forced with an IIT‐D model hindcast of the 2007 cyclone Sidr flood event, using parameters from two cyclone databases (IBTrACs and UNISYS). Validation showed inundation prediction accuracy with a root mean squared error (RMSE) on predicted water level of ∼ 2 m, which was of the same order of magnitude as the forcing water‐level uncertainties. Therefore, SRTM and other publicly available data can be useful for coastal flood risk management in data‐poor regions, although the associated uncertainty needs to be expressed to end users. Better SRTM processing techniques may improve inundation model performance, and future work should also seek to improve storm tide uncertainties in this region. Copyright © 2012 Royal Meteorological Society
The ethics of carbon offsetting
Authors: Hyams Keith , Fawcett Tina 
Published: January 2013

AbstractCarbon offsetting can be loosely characterized as a mechanism by which an organization or individual contributes to a scheme that is projected either to remove carbon dioxide from the atmosphere or to deliver carbon dioxide emission reductions on the part of other organizations or individuals. An activity that has been offset therefore purports to make no long‐term net contribution to atmospheric greenhouse gas concentrations. The ethical basis for using carbon offsetting as an approach to tackling climate change is very much contested. We seek to expose some of the underlying reasons for these ethical disagreements. We show that they relate both to empirical disagreements about what the likely benefits of offsetting are and, more fundamentally, to principled disagreements about the right way to discharge duties to deliver carbon reductions. WIREs Clim Change 2013, 4:91–98. doi: 10.1002/wcc.207This article is categorized under:

Climate, Nature, and Ethics > Ethics and Climate Change
Behaving badly or goodly: Is it because I feel guilty, shameful, or sympathetic? Or is it a matter of what I think?
Authors: Carlo Gustavo , McGinley Meredith , Davis Alexandra , Streit Cara 
Published: January 2013

AbstractThe article provides a brief review of theory and research on the roles of guilt, shame, and sympathy in predicting moral behaviors. Two models are presented and contrasted. The guilt‐based model proposes that guilt and shame jointly predict prosocial and aggressive behaviors. In contrast, the sympathy‐based model suggests that perspective taking and sympathy are linked to such behaviors. In both models, prosocial moral reasoning is proposed as a possible mediator in these relations. Results from a study of college students suggest support for both models. Moreover, there is evidence that prosocial moral reasoning mediates the relations between these moral emotions and moral behaviors. The implications for the need to incorporate moral emotions and cognitions into existing models of morality are discussed and emphasized.
Poverty in Global Perspective: Is Shame a Common Denominator?
Authors: WALKER ROBERT , KYOMUHENDO GRACE BANTEBYA , CHASE ELAINE , CHOUDHRY SOHAIL , GUBRIUM ERIKA K. , NICOLA JO YONGMIE , LØDEMEL IVAR , MATHEW LEEMAMOL , MWIINE AMON , PELLISSERY SONY , MING YAN 
Published: January 2013

AbstractFocussing on the psychosocial dimensions of poverty, the contention that shame lies at the ‘irreducible absolutist core’ of the idea of poverty is examined through qualitative research with adults and children experiencing poverty in diverse settings in seven countries: rural Uganda and India; urban China; Pakistan; South Korea and United Kingdom; and small town and urban Norway. Accounts of the lived experience of poverty were found to be very similar, despite massive disparities in material circumstances associated with locally defined poverty lines, suggesting that relative notions of poverty are an appropriate basis for international comparisons. Though socially and culturally nuanced, shame was found to be associated with poverty in each location, variably leading to pretence, withdrawal, self-loathing, ‘othering’, despair, depression, thoughts of suicide and generally to reductions in personal efficacy. While internally felt, poverty-related shame was equally imposed by the attitudes and behaviour of those not in poverty, framed by public discourse and influenced by the objectives and implementation of anti-poverty policy. The evidence appears to confirm the negative consequences of shame, implicates it as a factor in increasing the persistence of poverty and suggests important implications for the framing, design and delivery of anti-poverty policies.
A bilingual–monolingual comparison of young children's vocabulary size: Evidence from comprehension and production
Authors: DE HOUWER ANNICK , BORNSTEIN MARC H. , PUTNICK DIANE L. 
Published: January 2013

ABSTRACTIt is often assumed that young bilinguals are lexically delayed in comparison to monolinguals. A comprehensive comparison of comprehension and production vocabulary in 31 firstborn bilingual and 30 matched monolingual children fails to find empirical foundation for this assumption. Several raters completed Dutch and French adaptations of the MacArthur Communicative Development Inventories for children aged 13 and 20 months. At 13 months, bilinguals understood more words than did monolinguals; at 20 months, monolinguals knew more Dutch words than did bilinguals (combining comprehension and production). There were no group differences for word production or for Dutch word comprehension. Both groups understood and produced the same number of lexicalized meanings; ratios of word comprehension to word production did not differ; interindividual variation was similar. This study underscores the importance of conducting bilingual–monolingual comparisons with matched groups and suggests that if individual bilingual children appear to be slow in early vocabulary development, reasons other than their bilingualism should be investigated.
Distribution, habitat and status of the new species Nonggang Babbler Stachyris nonggangensis
Authors: ZHAOTIAN LI , FANG ZHOU , ZHOU LU , AIWU JIANG , GANG YANG , CHENXING YU 
Published: January 2013

SummaryThe Nonggang Babbler Stachyris nonggangensisis a new species of Timaliidae which was discovered in the Sino-Vietnamese border region in 2008. The species was initially classified as “Near Threatened” on the IUCN Red List and was believed to occur only in Nonggang Nature Reserve, where the type specimen was collected and where c.200 individuals were recorded. These few observations, and suggestions of a declining population, prompted us to initiate an extensive survey over the whole potential distribution range of this species in China from June 2009 to May 2011, during both dry and wet seasons. We conducted the survey in Guangxi Zhuang Autonomous Region and Yunnan Province and selected 19 reserves and forest areas where similar habitat to that in the Nonggang Reserve is known to occur. We used transects combined with playback to survey for this species. Nonggang Babbler was recorded at four new sites in the Sino-Vietnamese border region: two areas of the Nonggang Reserve (Nonggang and Longhu), Bangliang Gibbon Nature Reserve and Chunxiu Nature Reserve. The estimated population size of Nonggang Babbler was about 1,300 individuals in the four sites. Nonggang Babbler is also assumed to occur in the Trung Khanh Gibbon Reserve of Vietnam which adjoins Bangliang Gibbon Reserve. The estimated population in Trung Khanh is c.200 individuals. In total we estimate that the global population size of Nonggang Babbler is c.1,500 individuals. The Nonggang Babbler is restricted to karst forests, and its activities, foraging and nesting strictly rely on this habitat. Habitat loss and fragmentation are the main threats.
ALG-2-interacting Tubby-like protein superfamily member PLSCR3 is secreted by an exosomal pathway and taken up by recipient cultured cells
Authors: Inuzuka Tatsutoshi , Inokawa Akira , Chen Cen , Kizu Kumiko , Narita Hiroshi , Shibata Hideki , Maki Masatoshi 
Published: January 2013

PLSCRs (phospholipid scramblases) are palmitoylated membrane-associating proteins. Regardless of the given names, their physiological functions are not clear and thought to be unrelated to phospholipid scrambling activities observed in vitro. Using a previously established cell line of HEK-293 (human embryonic kidney-293) cells constitutively expressing human Scr3 (PLSCR3) that interacts with ALG-2 (apoptosis-linked gene 2) Ca2+-dependently, we found that Scr3 was secreted into the culture medium. Secretion of Scr3 was suppressed by 2-BP (2-bromopalmitate, a palmitoylation inhibitor) and by GW4869 (an inhibitor of ceramide synthesis). Secreted Scr3 was recovered in exosomal fractions by sucrose density gradient centrifugation. Palmitoylation sites and the N-terminal Pro-rich region were necessary for efficient secretion, but ABSs (ALG-2-binding sites) were dispensable. Overexpression of GFP (green fluorescent protein)-fused VPS4BE235Q, a dominant negative mutant of an AAA (ATPase associated with various cellular activities) ATPase with a defect in disassembling ESCRT (endosomal sorting complex required for transport)-III subunits, significantly reduced secretion of Scr3. Immunofluorescence microscopic analyses showed that Scr3 was largely localized to enlarged endosomes induced by overexpression of a GFP-fused constitutive active mutant of Rab5A (GFP–Rab5AQ79L). Secreted Scr3 was taken up by HeLa cells, suggesting that Scr3 functions as a cell-to-cell transferable modulator carried by exosomes in a paracrine manner.
Mediating free glucocorticoid levels in the blood of vertebrates: are corticosteroid‐binding proteins always necessary?
Authors: Desantis Lanna M. , Delehanty Brendan , Weir Jason T. , Boonstra Rudy 
Published: January 2013

Summary

Glucocorticoids (GC) are integral to the stress response of vertebrates to environmental challenges. Their impact is immediate and widespread, and prolonged exposure can result in major activational and organizational changes. The vertebrate body has two mechanisms to limit GC impact: first, a rapid negative feedback system to turn off their release, and second, a protein – corticosteroid‐binding globulin (CBG) – to prevent them being free in the blood. Species used in biomedical research have CBG levels that normally bind 90–95% of blood GC. This evidence was the basis for the ‘Free Hormone Hypothesis,’ which posits that only unbound, free hormone is available for use by tissues and is biologically active. High levels of free GC typically occur only under conditions of chronic stress and are associated with major suppression of key body functions. The hypothesis proposes that the primary role of CBG is to render GCs unavailable, thereby preventing tissue exposure.

From a field study in southern Ontario on northern (Glaucomys sabrinus) and southern (Glaucomys volans) flying squirrels, we found virtually no CBG binding capacity in their plasma, resulting in only about 10% of cortisol being bound throughout the year. However, neither species showed any evidence of being physiologically compromised. This presents a major challenge to the potential consequences of chronically high levels of free GC.

To assess the generality of this finding, we carried out a phylogenetic comparison of 91 vertebrate species in which both GC and CBG levels were measured. In 93%, CBG levels were sufficient to bind about 90% of circulating GCs. This evidence is thus concordant with that from biomedical research. However, both flying squirrel species and four species of New World monkeys were extreme outliers. These two groups had the highest GC concentrations, but relatively little binding capacity (10% or less of their GC was bound).

An ancestor state reconstruction of the proportion of GCs bound indicated that the flying squirrels and New World monkeys evolved this character state from ancestors that followed the common 90% bound pattern. It also indicated that the original vertebrates – the earliest fishes – have most of their GC in the free state and little or no steroid‐binding protein.

We thus demonstrate a dichotomous pattern with respect to CBG: a dominant branch, where high levels of CBG bind most of the GC, applies to the majority of vertebrates; and a secondary branch, where low levels of CBG bind almost none of the GC, applies to a very small subset. For the latter, the critical unknown is how these species mitigate the impact of the high free GC levels and how such a dramatic trait shift could evolve.
Specific jarosite biomineralization by Purpureocillium lilacinum, an acidophilic fungi isolated from Río Tinto
Authors: Oggerin M. , Tornos F. , Rodríguez N. , del Moral C. , Sánchez‐Román M. , Amils R. 
Published: January 2013

SummaryRío Tinto (Huelva, southwestern Spain) is an extreme environment with a remarkably constant acidic pH and a high concentration of heavy metals, conditions generated by the metabolic activity of chemolithotrophic microorganisms thriving in the rich complex sulfides of the Iberian Pyrite Belt (IPB). Fungal strains isolated from the Tinto basin were characterized morphologically and phylogenetically. The strain identified as Purpureocillium lilacinum specifically induced the formation of a yellow‐ocher precipitate, identified as hydronium‐jarosite, an iron sulfate mineral which appears in abundance on the banks of Río Tinto. The biomineral was characterized by X‐ray diffraction (XRD) and its formation was observed with high‐resolution transmission electron microscopy (TEM) and scanning electron microscopy (SEM) coupled to energy‐dispersive X‐ray spectroscopy (EDX) microanalysis. Jarosite began to nucleate on the fungal cell wall, associated to the EPS, due to a local increase in the Fe3+/Fe2+ ratio which generated supersaturation. Its formation has been also observed in non‐viable cells, although with much less efficiency. The occurrence of P. lilacinum in an ecosystem with high concentrations of ferric iron and sulfates such as Río Tinto suggests that it could participate in the process of jarosite precipitation, helping to shape and control the geochemical properties of this environment.
BLOG 2.0: a software system for character‐based species classification with DNA Barcode sequences. What it does, how to use it
Authors: Weitschek Emanuel , Van Velzen Robin , Felici Giovanni , Bertolazzi Paola 
Published: January 2013

AbstractBLOG (Barcoding with LOGic) is a diagnostic and character‐based DNA Barcode analysis method. Its aim is to classify specimens to species based on DNA Barcode sequences and on a supervised machine learning approach, using classification rules that compactly characterize species in terms of DNA Barcode locations of key diagnostic nucleotides. The BLOG 2.0 software, its fundamental modules, online/offline user interfaces and recent improvements are described. These improvements affect both methodology and software design, and lead to the availability of different releases on the website http://dmb.iasi.cnr.it/blog-downloads.php. Previous and new experimental tests show that BLOG 2.0 outperforms previous versions as well as other DNA Barcode analysis methods.