bluuebunny/crossref_metadata_2025_split huggingface dataset:
Site‐specific deamidation of glutamine: a new marker of bone collagen deterioration
Authors: van Doorn Nienke L. , Wilson Julie , Hollund Hege , Soressi Marie , Collins Matthew J. 
Published: September 2012

RATIONALENon‐enzymatic deamidation accumulates in aging tissues in vivo and has been proposed to be potentially useful as a molecular clock. The process continues post mortem, and here we explore the increase in levels of deamidation in archaeological collagen, as measured during Zooarchaeology by Mass Spectrometry (ZooMS) analysis.METHODSWith the high sensitivity of current generation mass spectrometers, ZooMS provides a non‐destructive and highly cost‐effective method to characterise collagen peptides. Deamidation can be detected by mass spectrometry as a +0.984 Da mass shift; therefore, aside from its original purpose, peptide mass‐fingerprinting for bone identification, ZooMS concurrently yields a 'thermal indicator' of the samples.RESULTSBy analysis of conventional ZooMS spectra, we determined the deamidation rate for glutamine residues in 911 bone collagen samples from 50 sites, with ages varying from medieval to Palaeolithic. The degree of deamidation was compared to diagenetic parameters and nearby sequence properties.CONCLUSIONSThe extent of deamidation was found to be influenced more by burial conditions and thermal age than, for example, chronological age, the extent of bioerosion or crystallinity. The method lends itself mostly to screening heterogenic deposits of bone to identify outliers. Copyright © 2012 John Wiley & Sons, Ltd.
Development of a Tuned Interfacial Force Field Parameter Set for the Simulation of Protein Adsorption to Silica Glass
Authors: Snyder James A. , Abramyan Tigran , Yancey Jeremy A. , Thyparambil Aby A. , Wei Yang , Stuart Steven J. , Latour Robert A. 
Published: September 2012

Adsorption free energies for eight host–guest peptides (TGTG-X-GTGT, with X = N, D, G, K, F, T, W, and V) on two different silica surfaces [quartz (100) and silica glass] were calculated using umbrella sampling and replica exchange molecular dynamics and compared with experimental values determined by atomic force microscopy. Using the CHARMM force field, adsorption free energies were found to be overestimated (i.e., too strongly adsorbing) by about 5–9 kcal/mol compared to the experimental data for both types of silica surfaces. Peptide adsorption behavior for the silica glass surface was then adjusted using a modified version of the CHARMM program, which we call dual force-field CHARMM, which allows separate sets of nonbonded parameters (i.e., partial charge and Lennard-Jones parameters) to be used to represent intra-phase and inter-phase interactions within a given molecular system. Using this program, interfacial force field (IFF) parameters for the peptide-silica glass systems were corrected to obtain adsorption free energies within about 0.5 kcal/mol of their respective experimental values, while IFF tuning for the quartz (100) surface remains for future work. The tuned IFF parameter set for silica glass will subsequently be used for simulations of protein adsorption behavior on silica glass with greater confidence in the balance between relative adsorption affinities of amino acid residues and the aqueous solution for the silica glass surface.
Childhood adversity and psychosis: Examining whether the association is due to genetic confounding using a monozygotic twin differences approach
Authors: Alemany S. , Goldberg X. , van Winkel R. , Gastó C. , Peralta V. , Fañanás L. 
Published: September 2012

AbstractPurposeTo test whether the association between childhood adversity and positive and negative psychotic experiences is due to genetic confounding.MethodChildhood adversity and psychotic experiences were assessed in an ongoing sample of 226 twins from the general population. A monozygotic (MZ) twin differences approach was used to assess possible genetic confounding.ResultsIn the whole sample, childhood adversity was significantly associated with positive (β = 45; SE = 0.16; P = 0.008) and negative psychotic experiences (β = 0.77; SE = 0.18; P < 0.01). Within-pair MZ twin differences in exposure to childhood adversity were significantly associated with differences in positive (β = 71; SE = 0.29; P = 0.016) and negative psychotic experiences (β = 98; SE = 0.38; P = 0.014) in a subsample of 85 MZ twin pairs.ConclusionsIndividuals exposed to childhood adversity are more likely to report psychotic experiences. Furthermore, our findings indicate that this association is not due to genetic confounding.
Reduced thalamic volume in men with antisocial personality disorder or schizophrenia and a history of serious violence and childhood abuse
Authors: Kumari V. , Gudjonsson G.H. , Raghuvanshi S. , Barkataki I. , Taylor P. , Sumich A. , Das K. , Kuipers E. , Ffytche D.H. , Das M. 
Published: September 2012

AbstractObjectiveViolent behaviour has been associated with presence of certain mental disorders, most notably antisocial personality disorder (ASPD) and schizophrenia, childhood abuse, and multiple brain abnormalities. This study examined for the first time, to the authors’ knowledge, the role of psychosocial deprivation (PSD), including childhood physical and sexual abuse, in structural brain volumes of violent individuals with ASPD or schizophrenia.MethodsFifty-six men (26 with ASPD or schizophrenia and a history of serious violence, 30 non-violent) underwent magnetic resonance imaging and were assessed on PSD. Stereological volumetric brain ratings were examined for group differences and their association with PSD ratings. PSD-brain associations were examined further using voxel-based-morphometry.ResultsThe findings revealed: reduced thalamic volume in psychosocially-deprived violent individuals, relative to non-deprived violent individuals and healthy controls; negative association between thalamic volume and abuse ratings (physical and sexual) in violent individuals; and trend-level negative associations between PSD and hippocampal and prefrontal volumes in non-violent individuals. The voxel-based-morphometry analysis detected a negative association between PSD and localised grey matter volumes in the left inferior frontal region across all individuals, and additionally in the left middle frontal and precentral gyri in non-violent individuals.ConclusionsViolent mentally-disordered individuals with PSD, relative to those with no or minimal PSD, suffer from an additional brain deficit, i.e., reduced thalamic volume; this may affect sensory information processing, and have implications for management, of these individuals. PSD may have a stronger relationship with volumetric loss of stress-linked regions, namely the frontal cortex, in non-violent individuals.
Peer and family influence in eating disorders: A meta-analysis
Authors: Quiles Marcos Y. , Quiles Sebastián M.J. , Pamies Aubalat L. , Botella Ausina J. , Treasure J. 
Published: September 2012

AbstractObjectiveThe aim of the present study was to undertake a systematic review using meta-analysis procedures to assess the relationships between eating disorders and peer and family influence and to evaluate whether gender plays a moderator role in that relationship.MethodPsycINFO, Medline, Web of Science, EPSCO and Embase databases from 1980 to 2010 were searched in June and October 2010. Hand searching of relevant reference sections was also undertaken.ResultsIt was possible to obtain 83 effect sizes from the 25 studies selected. Results showed that both peers and family influence dieting behavior, body dissatisfaction and bulimic symptoms in adolescent girls and boys. Furthermore, the analyses of the moderator variables showed that the variability of the effect sizes found was, in some cases, explained by gender, influence type and the country of the sample.Discussion and conclusionThese results highlight how daily social interactions can influence unhealthy eating practices in adolescent girls and boys, and suggest that weight-related issues of parents and peers can be transmitted to adolescents.
Maternal and perinatal outcome in cases of fulminant viral hepatitis in late pregnancy
Authors: Deng Liuzhi , Li Xiaomao , Shi Zhongjie , Jiang Peiru , Chen Dunjin , Ma Lin 
Published: September 2012

AbstractObjectiveTo investigate maternal and perinatal outcomes in cases of fulminant viral hepatitis in late pregnancy (FVHILP).MethodsA multicenter retrospective study was conducted. The records of 40 patients with FVHILP were retrieved from 3 hospitals in China. To analyze the influence of mode of delivery on maternal and perinatal outcomes, women were allocated to the cesarean delivery group or the spontaneous vaginal delivery (SVD) group. To study the relationship between maternal outcome and perinatal outcome, patients were allocated to the maternal survival group or the non‐survival group.ResultsThere were no significant differences between the cesarean group and the SVD group in clinical manifestations or laboratory indices before delivery, or in fatality rate (P > 0.05 for all), whereas there were significant differences in newborn weight, 1‐minute Apgar score, and incidence of severe perinatal asphyxia between the maternal survival group and the non‐survival group (P < 0.05 for all).ConclusionMaternal and perinatal outcomes in cases of FVHILP were not influenced by mode of delivery, whereas perinatal outcome significantly correlated with maternal outcome.
Structural and magnetic microinhomogeneities in accessory spinel of the system Fe2+(Cr2–xFex3+)O4 from the Kytlym massif (Urals platinum-bearing belt)
Authors: Sherendo T.A. , Martyshko P.S. , Moloshag V.P. , Garaeva A.A. , Zamyatin D.A. , Mitrofanov V.Ya. , Pamyatnykh L.A. 
Published: September 2012

Abstract
The microstructure and magnetic properties of accessory Fe–Cr-spinels from the Kytlym massif of the Urals platinum-bearing belt were studied. Atypical Fe–Cr-spinels in the form of magnetic microareas in grains of primary nonmagnetic Fe–Cr-spinel have been revealed for the first time in the bed dunites of the Kytlym multiphase concentrically zoned massif, North Urals. These spinels are responsible for the magnetic properties of the dunites. It has been established that the microareas are separations in solid solution Fe2+(Cr2–xFex3+)O4, which are enriched in Fe3+ and are probably an intermediate product of the transformation of primary accessory Fe-Cr-spinel during the formation of the dunite massif. These are magnetic microphases with particular chemical composition, cation distribution, and corresponding reversed crystal lattice, which determine the main magnetic properties of the microarea: the magnitude and direction of magnetization vector and Curie temperature. The formation of this earlier unknown type of magnetic Fe–Cr-spinel is probably conjugate with the formation and concentration of PGE mineralization in the bed dunites of the Kytlym platinum-bearing massif. The presence of such magnetization carriers in rocks and ores must be taken into account in geophysical research at the Urals chromite and platinum–chromite deposits.
Paleomagnetism of the Cretaceous sediments of the southern West Siberian Plate (from well 8 core studies)
Authors: Gnibidenko Z.N. , Lebedeva N.K. , Shurygin B.N. 
Published: September 2012

Abstract
The paper presents magnetobiostratigraphical data on the Cretaceous sediments stripped by well 8 in the southern side of the Om’ basin within the Om’–Lar’yak facies zone (southern West Siberia). The biostratigraphical data show that the sediments under study formed in the Albian–Maastrichtian. The componential analysis of natural remanent magnetization, based on thermal demagnetization and demagnetization with an alternating magnetic field, revealed the characteristic magnetization component. This confirms the paleomagnetic data used to compile the Cretaceous paleomagnetic section of the well. A paleomagnetic description was obtained, and a magnetobiostratigraphic key section of the Cretaceous sediments of the well was compiled on the basis of comprehensive data. It comprises five Upper Cretaceous regional horizons and same-named formations (Pokur, Kuznetsovo, Ipatovo, Slavgorod, Gan’kino), which have not been studied paleomagnetically at all in West Siberia. The magnetobiostratigraphic section comprises Albian–Maastrichtian stratigraphic units (43.5 Myr) and consists of three magnetozones. For example, the Pokur, Kuznetsovo, and Ipatovo Formations (total thickness 210 m), which show normal polarity with small reversed-magnetization horizons, form one long normal-polarity zone, N(al-st). The Slavgorod and Gan’kino Formations (total thickness 75 m), separated by a sedimentation gap, form two reversed-polarity magnetozones, R1(km) and R2(mt).
Reference datums (paleontologically well-constrained magnetozones) were used to correlate the magnetobiostratigraphic section with the common magnetostratigraphic and magnetochronologic scales. The long normal-polarity magnetozone N(al-st), spanning the Albian, Cenomanian, Turonian, Coniacian, and Santonian, matches the Dzhalal hyperzone and chron C34 (∼ 112–83.6 Ma). The reversed-polarity zones, spanning most of the Campanian (R1(km) (Slavgorod Formation)) and Maastrichtian (R2(mt) (Gan’kino Formation)), match chrons C33(r) and C31(r) in the absolute chronology (∼ 83.6–80 and 71–68.5 Ma, respectively) with a gap two chrons long (C33(n), C32).
Seismic-hazard assessment for Ulaanbaatar (Mongolia) on the basis of seismogeological studies
Authors: Imaev V.S. , Smekalin O.P. , Strom A.L. , Chipizubov A.V. , Syas’ko A.A. 
Published: September 2012

AbstractThe Gunzhin Fault is a tectonic structure in the southern Hentiyn arched uplift (central Mongolia). A fragment of this fault, exposed by two paleoearthquakes, is traced northeastward for ~25 km from the northern periphery of Ulaanbaatar. The first comprehensive seismogeological studies here were aimed at determining the seismic potential of seismogenic structures on the basis of the dislocation parameters. Judging by the strain amplitudes and length, earthquakes with a magnitude of &gt;7.0 might be generated here. The paleoearthquake was dated by the radiocarbon method at 7800–4667 B.C. Seismogenic zones with a high seismic potential were identified in central Mongolia for the first time. Dextral strike-slip faults were observed here among active NE-trending faults, suggesting the presence of E–W compressive stress.
Magneto-seismic studies of the eastern Qattara Depression, Northwestern desert, Egypt
Authors: Rabeh Taha 
Published: September 2012

Abstract
The potential field data are considered the main supporting factor in the geophysical exploration process for detecting and evaluating the subsurface structures. Therefore, a detailed land magnetic survey was performed in an area subjected to seismic investigations. The main target of this study was to detect the deeper subsurface structures and to investigate their possible relationships with earthquake activity.
The RTP aeromagnetic map was used to detect the regional extension of the structures interpreted from the land magnetic survey. The RTP land and aeromagnetic maps were interpreted by the filtering technique, least-squares separations, tectonic trend analysis, spectral analysis, Werner method, Euler method, and 2D techniques. The results show that the main tectonic trends are 35° N–45° W, 45° N–65° E, E–W, and Aqaba.
Moreover, two seismic lines, WQ85-31B and 127, were interpreted, and their location was matched with the deduced tectonic map. The results show great matching between the location of the faults deduced from both the geomagnetic and seismic data. They agree completely with the well logging data.
Furthermore, these structures are correlated with the earthquake activities recorded by the Egyptian National Seismological Network (ENSN). The correlation implies that the studied area is more stable than other adjacent areas in the northern parts of Egypt close to the Mediterranean Sea and the Nile River Delta.
The ‘zoo’ of secondary instabilities precursory to stratified shear flow transition. Part 1 Shear aligned convection, pairing, and braid instabilities
Authors: Mashayek A. , Peltier W. R. 
Published: September 2012

AbstractWe study the competition between various secondary instabilities that co-exist in a preturbulent stratified parallel flow subject to Kelvin–Helmholtz instability. In particular, we investigate whether a secondary braid instability might emerge prior to the overturning of the statically unstable regions that develop in the cores of the primary Kelvin–Helmholtz billows. We identify two groups of instabilities on the braid. One group is a shear instability which extracts its energy from the background shear and is suppressed by the straining contribution of the background flow. The other group, which seems to have no precedent in the literature, includes phase-locked modes which grow at the stagnation point on the braid and are almost entirely driven by the straining contributions of the background flow. For the latter group, the braid shear has a negative influence on the growth rate. Our analysis demonstrates that the probability of finite-amplitude growth of both braid instabilities is enhanced with increasing Reynolds number and Richardson number. We also show that the possibility of emergence of braid instabilities decreases with the Prandtl number for the shear modes and increases for the stagnation point instabilities. Through detailed non-separable linear stability analysis, we show that both braid instabilities are fundamentally three dimensional with the shear modes being of small wavenumbers and the stagnation point modes dominating at large wavenumber.
From travelling waves to mild chaos: a supercritical bifurcation cascade in pipe flow
Authors: Mellibovsky F. , Eckhardt B. 
Published: September 2012

AbstractWe study numerically a succession of transitions in pipe Poiseuille flow that lead from simple travelling waves to waves with chaotic time-dependence. The waves at the origin of the bifurcation cascade are twofold azimuthally periodic, shift–reflect symmetric, and have a non-dimensional axial wavelength of $1. 927$ diameters. As the Reynolds number is increased, successive transitions result in a wide range of time-dependent solutions that include spiralling, modulated travelling, modulated spiralling, doubly modulated spiralling and mildly chaotic waves. Numerical evidence suggests that the latter spring from heteroclinic tangles of the stable and unstable invariant manifolds of two shift–reflect symmetric, modulated travelling waves. The chaotic set thus produced is confined to a limited range of Reynolds numbers, bounded by the occurrence of manifold tangencies. The subspace of discrete symmetry to which the states studied here belong makes many of the bifurcation and path-following investigations presented readily accessible. However, we expect that most of the phenomenology carries over to the full state space, thus suggesting a mechanism for the formation and break-up of invariant states that can give rise to chaotic dynamics.
II: Typology of Metal Shield Fittings
Authors: Dickinson Tania , Härke Heinrich 
Published: September 2012

The classification presented here is based on a multivariate analysis of the shield bosses from the Upper Thames region, carried out in 1975 (Dickinson 1976, 274–90, figs. 25–9). Intuitive methods had failed to work, just as they had probably failed for previous scholars, because shield bosses seem to lack strikingly obvious diagnostic features. By contrast, the adoption of an explicit and more broadly-based approach not only took advantage of the substantial sample, but also was well suited to the circumstances of the enquiry. Residual doubts, however, meant that the results were not published at the time, though others have found the system both useful and valid (e.g. Welch 1983, 136–40, where the essentials are summarized; Hirst 1985, 91) and Heinrich Härke (HH) also adopted it as a base for the dating of shield burials in the course of his research. There is little excuse, therefore, for withholding publication further, and it is presented here substantially as it was written then, save for some modifications and additions.The classification was devised as an aid to dating male graves in the context of a cultural-historical study of the Upper Thames cemeteries. Its aim was chronological order, and its principal assumption was that similarity of form reflected a similarity in time and space of production, use and final deposition. It was largely innocent of developments in the theoretical ramifications of artefact classification (e.g. Hill and Evans 1972; but see now especially Miller 1985), and no doubt both contains and obscures categories which have little or nothing to do with time and space: some of these are explored by HH later in this volume.
Protonation state of E71 in KcsA and its role for channel collapse and inactivation
Authors: Bhate Manasi P. , McDermott Ann E. 
Published: September 2012

The prototypical prokaryotic potassium channel KcsA alters its pore depending on the ambient potassium; at high potassium, it exists in a conductive form, and at low potassium, it collapses into a nonconductive structure with reduced ion occupancy. We present solid-state NMR studies of KcsA in which we test the hypothesis that an important channel-inactivation process, known as C-type inactivation, proceeds via a state similar to this collapsed state. We test this using an inactivation-resistant mutant E71A, and show that E71A is unable to collapse its pore at both low potassium and low pH, suggesting that the collapsed state is structurally similar to the inactivated state. We also show that E71A has a disordered selectivity filter. Using site-specific K
+
titrations, we detect a local change at E71 that is coupled to channel collapse at low K
+
. To gain more insight into this change, we site specifically measure the chemical shift tensors of the side-chain carboxyls of E71 and its hydrogen bond partner D80, and use the tensors to assign protonation states to E71 and D80 at high K
+
and neutral pH. Our measurements show that E71 is protonated at pH 7.5 and must have an unusually perturbed
pK
a
(> 7.5) suggesting that the change at E71 is a structural rearrangement rather than a protonation event. The results offer new mechanistic insights into why the widely used mutant KcsA–E71A does not inactivate and establish the ambient K
+
level as a means to populate the inactivated state of KcsA in a controlled way.
FSelector: a Ruby gem for feature selection
Authors: Cheng Tiejun , Wang Yanli , Bryant Stephen H. 
Published: September 2012

Abstract
Summary: The FSelector package contains a comprehensive list of feature selection algorithms for supporting bioinformatics and machine learning research. FSelector primarily collects and implements the filter type of feature selection techniques, which are computationally efficient for mining large datasets. In particular, FSelector allows ensemble feature selection that takes advantage of multiple feature selection algorithms to yield more robust results. FSelector also provides many useful auxiliary tools, including normalization, discretization and missing data imputation.
Availability: FSelector, written in the Ruby programming language, is free and open-source software that runs on all Ruby supporting platforms, including Windows, Linux and Mac OS X. FSelector is available from https://rubygems.org/gems/fselector and can be installed like a breeze via the command gem install fselector. The source code is available (https://github.com/need47/fselector) and is fully documented (http://rubydoc.info/gems/fselector/frames).
Contact: ywang@ncbi.nlm.nih.gov or bryant@ncbi.nlm.nih.gov
Supplementary Information: Supplementary data are available at Bioinformatics online.