bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mechanism of N10‐formyltetrahydrofolate synthetase derived from complexes with intermediates and inhibitors
Authors: Celeste Lesa R. , Chai Geqing , Bielak Magdalena , Minor Wladek , Lovelace Leslie L. , Lebioda Lukasz 
Published: November 2011

AbstractN10‐formyltetrahydrofolate synthetase (FTHFS) is a folate enzyme that catalyzes the formylation of tetrahydrofolate (THF) in an ATP dependent manner. Structures of FTHFS from the thermophilic homoacetogen, Moorella thermoacetica, complexed with (1) a catalytic intermediate—formylphosphate (XPO) and product—ADP; (2) with an inhibitory substrate analog–folate; (3) with XPO and an inhibitory THF analog, ZD9331, were used to analyze the enzyme mechanism. Nucleophilic attack of the formate ion on the gamma phosphate of ATP leads to the formation of XPO and the first product ADP. A channel that leads to the putative formate binding pocket allows for the binding of ATP and formate in random order. Formate binding is due to interactions with the gamma‐phosphate moiety of ATP and additionally to two hydrogen bonds from the backbone nitrogen of Ala276 and the side chain of Arg97. Upon ADP dissociation, XPO reorients and moves to the position previously occupied by the beta‐phosphate of ATP. Conformational changes that occur due to the XPO presence apparently allow for the recruitment of the third substrate, THF, with its pterin moiety positioned between Phe384 and Trp412. This position overlaps with that of the bound nucleoside, which is consistent with a catalytic mechanism hypothesis that FTHFS works via a sequential ping‐pong mechanism. More specifically, a random bi uni uni bi ping‐pong ter ter mechanism is proposed. Additionally, the native structure originally reported at a 2.5 Å resolution was redetermined at a 2.2 Å resolution.
Screening for Anti‐inflammatory and Bronchorelaxant Activities of 12 Commonly Used Chinese Herbal Medicines
Authors: Yue Grace G. L. , Chan Ben C. L. , Kwok Hin‐Fai , To Ming‐Ho , Hon Kam‐Lun , Fung Kwok‐Pui , Lau Clara B. S. , Leung Ping‐Chung 
Published: November 2011

The use of health supplements derived from medicinal herbs as self‐medication for the relief of respiratory tract pathology symptoms is increasing in Chinese communities as air pollution is worsening. Twelve herbs from two formulae of our previous studies were evaluated for their anti‐inflammatory, immunomodulatory and bronchorelaxant activities in this study. Among the extracts tested, those of Herba Schizonepetae and Radix Glycyrrhizae showed significant inhibitory effects on LPS‐induced nitric oxide production (p < 0.05) in mouse macrophage RAW264.7 cells, suggesting their anti‐inflammatory activities. Radix Scutellariae and Radix Glycyrrhizae extracts showed significant inhibitory effects on phytohaemagglutinin‐induced proliferation in human peripheral blood mononuclear cells (p < 0.05). These extracts also showed inhibition of TNF‐α, IFN‐γ and IL‐10 production. For the bronchorelaxant assay, Rhizoma Cynanchi Stauntonii and Radix Glycyrrhizae extracts showed potent attenuation of the acetylcholine‐ and carbachol‐induced contractions in rat trachea (p < 0.05), implying their relaxant activities.In conclusion, Herba Schizonepetae, Radix Glycyrrhizae, Radix Scutellariae and Rhizoma Cynanchi Stauntonii extracts were demonstrated to exert anti‐inflammatory, immunomodulatory and bronchorelaxant activities, which may help to ameliorate the symptoms of respiratory tract pathologies. The findings have thus provided some scientific evidence on the efficacy and mechanisms of action of these herbs, which are useful for the further development of clinical applications. Copyright © 2011 John Wiley & Sons, Ltd.
A novel support vector classifier for longitudinal high‐dimensional data and its application to neuroimaging data
Authors: Chen Shuo , DuBois Bowman F. 
Published: November 2011

AbstractRecent technological advances have made it possible for many studies to collect high dimensional data (HDD) longitudinally, for example, images collected during different scanning sessions. Such studies may yield temporal changes of selected features that, when incorporated with machine learning methods, are able to predict disease status or responses to a therapeutic treatment. Support vector machine (SVM) techniques are robust and effective tools well suited for the classification and prediction of HDD. However, current SVM methods for HDD analysis typically consider cross‐sectional data collected during one time period or session (e.g., baseline). We propose a novel support vector classifier (SVC) for longitudinal HDD that allows simultaneous estimation of the SVM separating hyperplane parameters and temporal trend parameters, which determine the optimal means to combine the longitudinal data for classification and prediction. Our approach is based on an augmented reproducing kernel function and uses quadratic programming for optimization. We demonstrate the use and potential advantages of our proposed methodology using a simulation study and a data example from the Alzheimer's disease Neuroimaging Initiative. The results indicate that our proposed method leverages the additional longitudinal information to achieve higher accuracy than methods using only cross‐sectional data and methods that combine longitudinal data by naively expanding the feature space. © 2011 Wiley Periodicals, Inc. Statistical Analysis and Data Mining 4: 604–611, 2011
Model‐based clustering of regression time series data via APECM—an AECM algorithm sung to an even faster beat
Authors: Chen Wei‐Chen , Maitra Ranjan 
Published: November 2011

AbstractWe propose a model‐based approach for clustering time series regression data in an unsupervised machine learning framework to identify groups under the assumption that each mixture component follows a Gaussian autoregressive regression model of order p. Given the number of groups, the traditional maximum likelihood approach of estimating the parameters using the expectation‐maximization (EM) algorithm can be employed, although it is computationally demanding. The somewhat fast “tune” to the EM “folk song” provided by the Alternating Expectation Conditional Maximization (AECM) algorithm can alleviate the problem to some extent. In this article, we develop an alternative partial expectation conditional maximization algorithm (APECM) that uses an additional data augmentation storage step to efficiently implement AECM for finite mixture models. Results on our simulation experiments show improved performance in both fewer numbers of iterations and computation time. The methodology is applied to the problem of clustering mutual funds data on the basis of their average annual per cent returns and in the presence of economic indicators. © 2011 Wiley Periodicals, Inc. Statistical Analysis and Data Mining 4: 567–578, 2011
High‐Voltage Nano‐oxidation in Deionized Water and Atmospheric Environments by Atomic Force Microscopy
Authors: Huang Jen‐Ching , Chen Chung‐Ming 
Published: November 2011

SummaryThis study used atomic force microscopy (AFM), metallic probes with a nanoscale tip, and high‐voltage generators to investigate the feasibility of high‐voltage nano‐oxidation processing in deionized water (DI water) and atmospheric environments. Researchers used a combination of wirecutting and electrochemical etching to transform a 20‐μm‐thick stainless steel sheet into a conductive metallic AFM probe with a tip radius of 60 nm, capable of withstanding high voltages. The combination of AFM, high‐voltage generators, and nanoscale metallic probes enabled nano‐oxidation processing at 200 V in DI water environments, producing oxides up to 66.6 nm in height and 467.03 nm in width. Oxides produced through highvoltage nano‐oxidation in atmospheric environments were 117.29 nm in height and 551.28 nm in width, considerably exceeding the dimensions of those produced in DI water. An increase in the applied bias voltage led to an apparent logarithmic increase in the height of the oxide dots in the range of 200‐400 V. The performance of the proposed high‐voltage nano‐oxidation technique was relatively high with seamless integration between the AFM machine and the metallic probe fabricated in this study. SCANNING 34: 230‐236, 2012 © 2011 Wiley Periodicals, Inc.
Performance analysis of secure beaconing messages for GeoNetworking
Authors: Lee Jong‐Hyouk , Ernst Thierry , Ma Xiaomin 
Published: November 2011

ABSTRACTGeoNetworking is a protocol specially designed to provide geographical addressing and forwarding for Cooperative Intelligent Transport Systems (ITS). Unlike advanced messages defined in GeoNetworking, beaconing messages are fundamental to periodically advertise essential information, e.g., a vehicle ITS station's geographical position and speed, to neighbor ITS stations. The beaconing messages should be delivered in a secure manner. Otherwise, geographical addressing and forwarding of GeoNetworking cannot be supported as unauthorized actions from attackers break down cooperative communication between ITS stations. However, security mechanisms for beaconing messages come with overhead that affect the overall performance. This being so, in this paper, we analyze the overhead of secure beaconing messages in terms of packet delivery ratio, delay, and normalized throughput. From the conducted numerical analysis, we demonstrate that 1) three parameters such as the number of ITS stations in a given radio range, the backoff window size, and the message size mainly affect the performance; 2) the delay of secure beaconing message is still acceptable with proper channel bit rates; and 3) the normalized throughput of secure beaconing message is better than that of the basic beaconing message. Copyright © 2011 John Wiley & Sons, Ltd.
Tailored Profiles Made of Tailor Rolled Strips by Roll Forming – Part 1 of 2
Authors: Hirt Gerhard , Dávalos‐Julca Daniel H. 
Published: November 2011

AbstractTo fully exploit the potential of sheet and profiles, various technologies to produce tailored blanks and profiles have been developed [1,2]. In earlier work [3] it has been shown that Strip Profile Rolling (SPR) can be used to produce metal strips with a predefined thickness distribution across the width of the strip. Building upon this knowledge, in two subsequent papers the extended goal of the project is presented. Therein is demonstrated that Strip Profile Rolling can be applied very effectively using a combination of roll forming (part 1) as well as further processing by roll forming (see part 2) to allow for the production of profiles with varying wall thickness in their cross section. To achieve the goal of part 1, a numerical model describing SPR was developed and used to study the influencing process parameters on spread and bulge formation. As a result of this parametric study, an optimized roll design and rolling sequence was developed to produce a demonstrator strip on a 12 stand roll forming mill manufactured by the company Dreistern [4]. Starting with a conventional strip out of DC01 steel (width 170 mm, thickness 2.5 mm), 29 rolling passes were necessary to achieve the desired geometry (width 186 mm, thickness 2.5 mm with a longitudinal groove being 64 mm wide where the thickness is reduced to 1.5 mm). In the second part of the process chain the coils produced by Strip Profile Rolling were successfully roll formed into a circular tube of 60 mm.
Status of Genomic Imprinting in Epigenetically Distinct Pluripotent Stem Cells
Authors: Sun Bowen , Ito Mitsuteru , Mendjan Sasha , Ito Yoko , Brons I. Gabrielle M. , Murrell Adele , Vallier Ludovic , Ferguson-Smith Anne C. , Pedersen Roger A. 
Published: November 2011

Abstract
Mouse epiblast stem cells (EpiSCs) derived from postimplantation embryos are developmentally and functionally different from embryonic stem cells (ESCs) generated from blastocysts. EpiSCs require Activin A and FGF2 signaling for self-renewal, similar to human ESCs (hESCs), while mouse ESCs require LIF and BMP4. Unlike ESCs, EpiSCs have undergone X-inactivation, similar to the tendency of hESCs. The shared self-renewal and X-inactivation properties of EpiSCs and hESCs suggest that they have an epigenetic state distinct from ESCs. This hypothesis predicts that EpiSCs would have monoallelic expression of most imprinted genes, like that observed in hESCs. Here, we confirm this prediction. By contrast, we find that mouse induced pluripotent stem cells (iPSCs) tend to lose imprinting similar to mouse ESCs. These findings reveal that iPSCs have an epigenetic status associated with their pluripotent state rather than their developmental origin. Our results also reinforce the view that hESCs and EpiSCs are in vitro counterparts, sharing an epigenetic status distinct from ESCs and iPSCs.
Disclosure of potential conflicts of interest is found at the end of this article.
Risikoberechnungen beim X-chromosomal rezessiven Erbgang
Authors: Grimm T. , Fischer C. 
Published: November 2011

Zusammenfassung
Am Beispiel der Muskeldystrophie Duchenne werden Risikoberechnungen beim X-chromosomal rezessiven Erbgang mithilfe des Bayesschen Rechentableaus durchgeführt und dabei demonstriert, wie sich auch komplexe genetische Modelle berücksichtigen lassen und auf das Risiko auswirken.
Deccan Volcanism Linked to the Cretaceous-Tertiary Boundary Mass Extinction: New Evidence from ONGC Wells in the Krishna-Godavari Basin
Authors: Keller G. , Bhowmick P.K. , Upadhyay H. , Dave A. , Reddy A.N. , Jaiprakash B.C. , Adatte T. 
Published: November 2011

Abstract
A scientific challenge is to assess the role of Deccan volcanism in the Cretaceous-Tertiary boundary (KTB) mass extinction. Here we report on the stratigraphy and biologic effects of Deccan volcanism in eleven deep wells from the Krishna-Godavari (K-G) Basin, Andhra Pradesh, India. In these wells, two phases of Deccan volcanism record the world’s largest and longest lava mega-flows interbedded in marine sediments in the K-G Basin about 1500 km from the main Deccan volcanic province. The main phase-2 eruptions (~80% of total Deccan Traps) began in C29r and ended at or near the KTB, an interval that spans planktic foraminiferal zones CF1-CF2 and most of the nannofossil Micula prinsii zone, and is correlative with the rapid global warming and subsequent cooling near the end of the Maastrichtian. The mass extinction began in phase-2 preceding the first of four mega-flows. Planktic foraminifera suffered a 50% drop in species richness. Survivors suffered another 50% drop after the first mega-flow, leaving just 7 to 8 survivor species. No recovery occurred between the next three mega-flows and the mass extinction was complete with the last phase-2 mega-flow at the KTB. The mass extinction was likely the consequence of rapid and massive volcanic CO2 and SO2 gas emissions, leading to high continental weathering rates, global warming, cooling, acid rains, ocean acidification and a carbon crisis in the marine environment.
Deccan volcanism phase-3 began in the early Danian near the C29R/C29n boundary correlative with the planktic foraminiferal zone P1a/P1b boundary and accounts for ~14% of the total volume of Deccan eruptions, including four of Earth’s longest and largest mega-flows. No major faunal changes are observed in the intertrappeans of zone P1b, which suggests that environmental conditions remained tolerable, volcanic eruptions were less intense and/or separated by longer time intervals thus preventing runaway effects. Alternatively, early Danian assemblages evolved in adaptation to high-stress conditions in the aftermath of the mass extinction and therefore survived phase-3 volcanism. Full marine biotic recovery did not occur until after Deccan phase-3. These data suggest that the catastrophic effects of phase-2 Deccan volcanism upon the Cretaceous planktic foraminifera were a function of both the rapid and massive volcanic eruptions and the highly specialized faunal assemblages prone to extinction in a changing environment. Data from the K-G Basin indicates that Deccan phase-2 alone could have caused the KTB mass extinction and that impacts may have had secondary effects.
Light Hydrocarbons Geochemistry of Surface Sediments from Pranhita-Godavari Basin, Andhra Pradesh
Authors: Anu Radha B. , Rasheed M. A. , Srinivasa Rao P.L. , Kalpana M.S. , Dayal A. M. 
Published: November 2011

Abstract
A geochemical study of surface sediments from Pranhita-Godavari Basin, Andhra Pradesh, India was carried out using light hydrocarbon compounds to assess the hydrocarbon potential of the basin. Suite of 80 soil samples were collected from the depth of 2.5 m and analyzed for adsorbed light gaseous hydrocarbons namely methane (CH4), ethane (C2H6) and propane (C3H8) in Gas chromatograph. Compound specific Carbon isotope ratios for CH4 and C2H6 were also determined using GC-C IRMS (Gas Chromatograph Combustion Isotope Mass Spectrometer). The presence of moderate to low concentrations of methane (CCH4: 1 to 138 ppb), ethane (CC2H6: 1 to 35 ppb) and propane (CC3H8: 1 to 20 ppb) was measured in the soil samples. Carbon isotopic composition of δ13CCH4 ranges between -27.9 to -47.1 ‰ and δ13CC2H6 ranged between -36.9 to -37.2 ‰ (V-PDB) indicating that these gases are of thermogenic origin. Study of soil samples suggests the area has good potential for hydrocarbon.
Flow-types and Lava Emplacement History of Rajahmundry Traps, West of River Godavari, Andhra Pradesh
Authors: Sen Bibhas , Sabale A. B. 
Published: November 2011

Abstract
Rajahmundry Traps has been under geo-scientific investigations for over half a century; yet sketchy information is available on morphology and internal architecture of lavas. This study bridges this gap by describing the morphology of lava pile of Duddukuru area following Hawaiian scheme that relates a lava-type with a particular emplacement style.
The lowest flow (Flow 1) at Duddukuru, overlying an infra-trappean bed is a thick pahoehoe sheet lobe with intermittent basal hummocky, P-type pahoehoe lobes representing slow, sub-aerial emplacement of lava parcels. Some of them also have cherty intercalations and morphology suggestive of possible interaction of lava with water or water-laden sediments. Hummocky lobes were over-ridden by subaerial emplacement of voluminous sheet lava, which developed multi-tier columnar joints probably due to inundation of lava-surface by water. Inter-trappean sediments were deposited above Flow 1 in the ensuing period of volcanic quiescence. The eruptive history of Duddukuru ended with sub-aerial outpouring of two consecutive a’a flows (Flows 2 and 3) separated by a thin red bole horizon.
As pahoehoe lavas are known to travel long distances due to emplacement through thermally efficient mechanism of endogenous inflation and insulated melt transport whereas a’a lavas, in contrast, are cooling-limited flows which rarely attain lengths covered by pahoehoe lavas; it is probable that the pahoehoe and a’a flows of Duddukuru have not traveled comparable distances. A’a flows of Rajahmundry Traps traveling from far-off vents are, therefore, more unlikely despite temporal and chemical similarity of this lava-pile with upper parts of Western Deccan Basalt Group.
Middleware for social computing: a roadmap
Authors: Capra Licia , Quercia Daniele 
Published: November 2011

AbstractSocial computing broadly refers to supporting social behaviours using computational systems. In the last decade, the advent of Web 2.0 and its social networking services, wikis, blogs, and social bookmarking has revolutionised social computing, creating new online contexts within which people interact socially (socialnetworking). With the pervasiveness of mobile devices and embedded sensors, we stand at the brink of another major revolution, where the boundary between online and offline social behaviours blurs, providing opportunities for (re)defining social conventions and contexts once again. But opportunities come with challenges: can middleware foster the engineering of social software? We identify threesocietalgrand challenges that are likely to drive future research in social computing and elaborate on how the middleware community can help address them.
Out of Sight, Out of Mind: Including Group Quarters Residents With Household Residents Can Change What We Know About Working-Age People With Disabilities
Authors: Stapleton David , Honeycutt Todd , Schechter Bruce 
Published: November 2011

AbstractInformation about residents of institutional and noninstitutional group quarters (GQ), particularly those with disabilities, has been limited by gaps in survey data, and statistics based on data that exclude some or all GQ residents are biased as estimates of total population statistics. We used the 2006 and 2007 American Community Survey (ACS) to identify the distribution of working-age populations with and without disabilities by major residence type and to assess the sensitivity of disability statistics to GQ residence. Our findings show that (1) of those with disabilities, about 1 in 13 males and 1 in 33 females live in GQ; (2) GQ rates are higher for individuals reporting mental, self-care, or go-outside-the-home disabilities than for those reporting sensory, physical, or employment disabilities; (3) younger males with disabilities are more likely to reside there, particularly at institutional GQ, reflecting their relatively high incarceration rate; (4) individuals with and without disabilities who are black, American Indian, were never married, or have less than a high school education have higher GQ residence rates; (5) 40% of male and 62% of female GQ residents have a disability; (6) adding GQ residents to household residents increases estimated disability prevalence for males by 6%, and the estimated difference between disability prevalence rates by gender nearly disappears; and (7) inclusion of the GQ population substantially lowers employment rate estimates for young males, blacks, and American Indians.
Relationship of Acetabular Dysplasia and Femoroacetabular Impingement to Hip Osteoarthritis: A Focused Review
Authors: Harris‐Hayes Marcie , Royer Nathaniel K. 
Published: November 2011

AbstractHip osteoarthritis (OA) leads to significant functional limitations and economic burden. If modifiable risk factors for hip OA are identified, it may be possible to implement preventative measures. Bony abnormalities associated with acetabular dysplasia (AD) and femoroacetabular impingement have been recently implicated as risk factors for hip OA. The purpose of this focused review is to summarize the available evidence describing the relationship between bony abnormalities and hip OA. A librarian‐assisted database search with PubMed, Embase, and CENTRAL was performed. Relevant articles were identified and assessed for inclusion criteria. The authors reviewed cohort and case‐control studies that reported on the association between abnormal hip morphology and hip OA. The available literature suggests that an association exists between bony abnormalities found in AD and femoroacetabular impingement and hip OA, and preliminary evidence suggests that AD is a risk factor for OA; however, these conclusions are based on limited evidence. Prospective, longitudinal studies are needed to confirm the causal relationship between abnormal hip morphology and the future development of hip OA.