bluuebunny/crossref_metadata_2025_split huggingface dataset:
Scoring function accuracy for membrane protein structure prediction
Authors: Gao Cen , Stern Harry A. 
Published: April 2007

AbstractWe perform a systematic examination of the ability of several different high‐resolution, atomic‐detail scoring functions to discriminate native conformations of loops in membrane proteins from non‐native but physically reasonable, or “decoy,” conformations. Decoys constructed from changing a loop conformation while keeping the remainder of the protein fixed are a challenging test of energy function accuracy. Nevertheless, the best of the energy functions we examined recognized the native structure as lowest in energy around half the time, and consistently chose it as a low‐energy structure. This suggests that the best of present energy functions, even without a representation of the lipid bilayer, are of sufficient accuracy to give reasonable confidence in predictions of membrane protein structure. We also constructed homology models for each structure, using other known structures in the same protein family as templates. Homology models were constructed using several scoring functions and modeling programs, but with a comparable sampling effort for each procedure. Our results indicate that the quality of sequence alignment is probably the most important factor in model accuracy for sequence identity from 20–40%; one can expect a reasonably accurate model for membrane proteins when sequence identity is greater than 30%, in agreement with previous studies. Most errors are localized in loop regions, which tend to be found outside the lipid bilayer. For the most discriminative energy functions, it appears that errors are most likely due to lack of sufficient sampling, although it should be stressed that present energy functions are still far from perfectly reliable. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Computational analysis of the S. cerevisiae proteome reveals the function and cellular localization of the least and most amyloidogenic proteins
Authors: Tartaglia Gian Gaetano , Caflisch Amedeo 
Published: April 2007

AbstractProtein sequences have evolved to optimize biological function that usually requires a well‐defined three‐dimensional structure and a monomeric (or oligomeric) state. These two requirements may be in conflict as the propensity for β‐sheet structure, which is one of the two most common regular conformations of the polypeptide chain in folded proteins, favors also the formation of ordered aggregates of multiple copies of the same protein (fibril, i.e., polymeric state). Such β‐aggregation is typical of amyloid diseases that include Alzheimer's, Parkinson's, and type II diabetes as well as the spongiform encephalopaties. Here, an analytical model previously developed for evaluating the amyloidogenic potential of polypeptides is applied to the proteome of the budding yeast (Saccharomyces cerevisiae). The model is based on the physicochemical properties that are relevant for β‐aggregation and requires only the protein sequence as input. It is shown that β‐aggregation prone proteins in yeast are accrued in molecular transport, protein biosynthesis, and cell wall organization processes while they are underrepresented in ribosome biogenesis, RNA metabolism, and vitamin metabolism. Furthermore, β‐aggregation prone proteins are much more abundant in the cell wall, endoplasmic reticulum, and plasma membrane than in the nucleolus, ribosome, and nucleus. Thus, this study indicates that evolution has not only prevented the selection of amyloidogenic sequences in cellular compartments characterized by a high concentration of unfolded proteins but also tried to exploit the β‐aggregated state for certain functions (e.g. molecular transport) and in well‐confined cellular environments or organelles to protect the rest of the cell from toxic (pre‐)fibrillar species. Proteins 2007. © 2007 Wiley‐Liss, Inc.
Rotigotine: first dopamine agonist transdermal patch
Authors: Metta Vinod , Muzerengi Sharon , Chaudhuri K Ray 
Published: April 2007

AbstractRotigotine (Neupro) is the first dopamine agonist skin patch to become available. Our New products review considers the clinical‐trial evidence for its efficacy and tolerability in the treatment of early and advanced Parkinson's disease. Copyright © 2007 Wiley Interface Ltd
Nongenital warts: recommended approaches to management
Authors: Shankar Sonal , Sterling Jane 
Published: April 2007

AbstractAlthough warts usually resolve sponta neously in time, patients often request treat ment due to discomfort or their appearance. Our Drug review considers the properties and efficacy of the many treatments avail able, followed by sources of further informa tion and the Datafile. Copyright © 2007 Wiley Interface Ltd
Fluorescence analysis of dissolved organic matter in natural, waste and polluted waters—a review
Authors: Hudson Naomi , Baker Andy , Reynolds Darren 
Published: April 2007

AbstractDissolved organic matter (DOM) in aquatic systems originates from a range of sources. Some is allochthonous, transported from the surrounding landscape to the water body, and is derived from and influenced by the geology, land use and hydrology of its origin. Some is created in situ through microbial activity, which may provide an independent source of organic matter, or a recycling mechanism for that which has been transported into the water body. The relative contribution of each source depends upon the location and environmental conditions within and without the water body. Human activity is also a source of DOM, much of which is believed to be labile, which can enter the aquatic system through direct point discharges, diffuse leaching and aerial dispersal. Fluorescence spectroscopy can provide an excellent tool to source DOM fractions, and to monitor and understand DOM transformations in aquatic systems, as much DOM has an intrinsic fluorescence. In particular, recent advances in optical technology, enabling rapid investigation of shorter wavelengths, have enabled more detailed characterization of organic material and its reactions in water. In this article, we review the use of fluorescence spectroscopic techniques to measure the intrinsic fluorescence of organic matter and the application of fluorescent DOM analysis in marine waters, freshwaters and wastewaters. Copyright © 2007 John Wiley & Sons, Ltd.
Atomic simulation of the point defects in three low‐index surfaces of BCC transition metals with the MAEAM
Authors: Zhang Jian‐Min , Wen Yan‐Ni , Xu Ke‐Wei 
Published: April 2007

AbstractThe favorable position of an adatom and the formation energies of a single vacancy and an adatom‐vacancy pair in three low‐index surfaces of body‐centered cubic (BCC) transition metals have been calculated by using the modified analytical embedded atom method (MAEAM). The favorable position of an adatom is at the fourfold and twofold positions above the (100) and (110) surfaces respectively, but it is deviated $(3 - \sqrt{6})a/3$ from the threefold position of the (111) surface. Either the heights of the adatom from the top atomic layer, or the formation energies of a single vacancy, or an adatom‐vacancy pair decrease in sequence of the (110), (100) and (111) surfaces for each metal. Furthermore, the formation energy of an adatom‐vacancy pair is always lower than that of a single vacancy for each low‐index surface of each metal, which shown the formation of adatom‐vacancy pair is more energetically favorable than the vacancy for the BCC transition metals. Copyright © 2007 John Wiley & Sons, Ltd.
How national systems differ in their constraints on corporate executives: a study of CEO effects in three countries
Authors: Crossland Craig , Hambrick Donald C. 
Published: April 2007

AbstractDo CEOs matter more in some countries than in others? Based on a theoretical consideration of three fundamental national‐level institutions—national values, prevailing firm ownership structures, and board governance arrangements—we argue that CEOs in different countries face systematically different degrees of constraint on their latitudes of action, and hence they differ in how much effect they have on firm performance. To test these ideas, we apply a variance components analysis methodology to 15‐year matched samples of 100 U.S. firms, 100 German firms, and 100 Japanese firms. Results provide strong, robust evidence that the effect of CEOs on firm performance—for good and for ill—is substantially greater in U.S. firms than in German and Japanese firms. Copyright © 2007 John Wiley & Sons, Ltd.
Practical testing of a C99 compiler using output comparison
Authors: Sheridan Flash 
Published: April 2007

AbstractA simple technique is presented for testing a C99 compiler, by comparing its output with the output from pre‐existing tools. The advantage to this approach is that new test cases can be added in bulk from existing sources, reducing the need for in‐depth investigation of correctness issues and for creating new test code by hand. This technique was used in testing the PalmSource Palm OS® Cobalt ARM C/C++ cross‐compiler for Palm‐Powered® personal digital assistants, primarily for standards compliance and the correct execution of generated code. The technique described here found several hundred bugs, mostly in our in‐house code, but also in longstanding high‐quality front‐ and back‐end code from Edison Design Group and Apogee Software. It also found 18 bugs in the GNU C compiler, as well as a bug specific to the Apple version of GCC, a bug specific to the Suse version of GCC, and a dozen bugs in versions of GCC for the ARM processor, several of which were critical. Copyright © 2007 John Wiley & Sons, Ltd.
When to use splay trees
Authors: Lee Eric K. , Martel Charles U. 
Published: April 2007

AbstractIn this paper we present new empirical results for splay trees. These results provide a better understanding of how cache performance affects query execution time. Our results show that splay trees can have faster lookup times compared with randomly built binary search trees (BST) under certain settings. In contrast, previous experiments have shown that because of the instruction overhead involved in splaying, splay trees are less efficient in answering queries than randomly built BSTs—even when the data sets are heavily skewed (a favorable setting for splay trees). We show that at large tree sizes the difference in cache performance between the two types of trees is significant. This difference means that splay trees are faster than BSTs for this setting—despite still having a higher instruction count. Based on these results we offer guidelines in terms of tree size, access pattern, and cache size as to when splay trees will likely be more efficient. We also present a new splaying heuristic aimed at reducing instruction count and show that it can improve on standard splaying by 10–27%. Copyright © 2007 John Wiley & Sons, Ltd.
Clock synchronization for distributed media applications
Authors: Distler Thomas James , Ouyang Jinsong 
Published: April 2007

AbstractCurrent video wall technology relies on custom processing hardware to drive the individual display channels. This hardware is both expensive to design and to maintain. Given that modern off‐the‐shelf computers have a significant amount of computing power, future video displays can be driven with this hardware at a lower cost. By using mass‐produced computers and a standard commercial operating system, the benefits of economies of scale can be brought to the custom video wall market. This paper describes a Windows library that provides the synchronized timing support necessary to drive a video wall with consumer hardware. The goal is to provide a key building block for the media software that will process the incoming video stream. This library exports several interfaces to the host software and provides support for synchronized timers, a synchronized clock, and reliable multicast messaging. The library uses common Windows APIs and protocols for maximum interoperability and portability. Through empirical testing, we are able to show that synchronization between any two machines in the system can be maintained to within 12 ms when run on Windows XP SP2. This synchronization is also shown to be consistent even when there is a heavy load on the processor. As a result, this library will successfully allow a commercial video wall to be driven from media software running on consumer hardware and software. Copyright © 2007 John Wiley & Sons, Ltd.
Low citrulline may not be diagnostic of ornithine transcarbamylase deficiency: A case report
Authors: Chiong M. A. , Carpenter K. , Christodoulou J. 
Published: April 2007

SummaryA newborn boy with family history of severe ornithine transcarbamylase (OTC) deficiency was investigated prospectively and managed aggressively at birth based on an existing protocol for at risk neonates. Undetectable citrulline levels at birth suggested that the infant was affected; however, normal plasma glutamine and urine orotic acid levels confused the diagnosis to some extent. Mutation testing confirmed that the patient did not have OTC deficiency. Thus the low plasma citrulline level did not validate our initial biochemical suspicion of OTC deficiency, and this highlights the importance of considering all available clinical, biochemical and molecular evidence in determining disease status.
Diagnostic criteria for CRPS I: Differences between patient profiles using three different diagnostic sets
Authors: Perez Roberto S.G.M. , Collins Susan , Marinus Johan , Zuurmond Wouter W.A. , de Lange Jaap J. 
Published: April 2007

AbstractComplex Regional Pain Syndrome type I (CRPS I) is an illness which usually occurs due to major or minor tissue injury to the extremities. Because a unique pathophysiological mechanism for CRPS I has not yet been established, the diagnosis is based on observation and measurement of clinical symptoms and signs. In this study, a comparison was made between three sets of diagnostic criteria (the IASP, Bruehl et al. and Veldman et al.) based on patient reports and physicians’ assessments of signs and symptoms associated with CRPS I, in 372 outpatients suspected of having CRPS I. Agreement between CRPS I diagnosis among the three sets was poor (κ‐range: 0.29–0.42), leading to positive CRPS I diagnoses according to Veldman et al.'s criteria in 218 cases (59%), according to the IASP in 268 cases (72%), and according to Bruehl et al. in 129 cases (35%). Significant differences in patient profiles were found between the diagnostic sets for the number of patients reporting continuing disproportionate pain, larger area affected than the initial trauma (both p<0.001), increase of symptoms due to exercise (p=0.009), edema (p=0.015), temperature asymmetry (p=0.015), hyperesthesia, allodynia (both p<0.001) and hyperalgesia (p=0.036). Similarly, significant differences emerged for physicians’ observations of hyperesthesia and allodynia (both p<0.001). Highest combined values of sensitivity (SE) and specificity (SP) for the strongest cases of presence (n=108) or absence (n=62) of CRPS I were found for reported hyperesthesia (SE+SP:165%), allodynia (160%), observed color asymmetry (162%), hyperesthesia (157%), temperature asymmetry (154%) and edema (152%). The lack of agreement between the different diagnostic sets for CRPS I and the different clinical profiles that result from it may lead to different therapeutic and study populations, hampering adequate treatment and scientific development for this illness. We propose explicit reference to diagnostic criteria used in studies, and registration in trials of a broad variety of CRPS I features, as used in this study, to make subgroup phenotyping and post hoc analyses based on different diagnostic criteria possible.
Submarine push moraine formation during the early Fennoscandian Ice Sheet deglaciation
Authors: Laberg J.S. , Eilertsen R.S. , Salomonsen G.R. , Vorren T.O. 
Published: April 2007

AbstractThe glacial history in the topographically confined paleo-ice stream drainage route of Vestfjorden, North Norway, was analysed based on bathymetric data, high-resolution seismology and 14C AMS-dated gravity cores. The inner part of the fjord is characterised by axial-parallel mega-scale lineations whereas the outer part is dominated by two marginal morainal bank systems. The Værøy (inner) and Røst (outer) marginal moraine systems comprise several transverse, zigzag-shaped ridges. Seismic records show thrusted and folded sediment blocks within the ridges. The landforms are inferred to reflect basal processes and the transition from warm-based (inner fjord) to cold-based (outer fjord) conditions, i.e. fast flow followed by basal freeze-on, sediment deformation and morainal bank formation. The moraines formed during the final part of two paleo-ice sheet re-advances. 14C AMS dating indicates a maximum age of 13.7 14C ka BP (16.2 cal ka BP) for the Røst system whereas the Værøy system is inferred to be slightly older than 12.5 14C ka BP (14.5 cal ka BP). This demonstrates that the northern part of the Fennoscandian Ice Sheet behaved in a much more dynamic way during the early deglaciation than previously assumed.
Food chromium content, dietary chromium intake and related biological variables in French free-living elderly
Authors: Roussel Anne-Marie , Andriollo-Sanchez Maud , Ferry Monique , Bryden Noella A. , Anderson Richard A. 
Published: April 2007

Trivalent chromium (Cr3+) is an essential trace element involved in insulin function. Cr deficiencies result in decreased insulin sensitivity, glucose intolerance and an increased risk of diabetes. Cr status decreases with age suggesting that the elderly may be at high risk of Cr deficiency. This study aimed to provide information about the Cr content of foods in France and the Cr intake in French free-living elderly. We measured the food Cr content and daily Cr intake of freely chosen diets for 3 d in twelve French free-living elderly people and their Cr excretion and plasma hormonal related variables, leptin, insulin and cortisol. Considering the relationship between insulin resistance and oxidative stress, we also determined plasma thiobarbituric acid reactive substance, thiol groups and total and reduced glutathione. Although these subjects had well-balanced diets, their daily Cr intakes did not reach the French recommendations. The low Cr intakes were due to the low Cr density of the foods. We found a negative correlation between Cr intakes and insulin, BMI and leptin.
Oropharyngeal and hypopharyngeal myxoma: case report and literature review
Authors: Ayache S , Chatelain D , Tramier B , Strunski V 
Published: April 2007

Objectives: To describe the features of an oropharyngeal and hypopharyngeal myxoma.Materials and methods: Case report of a 34-year-old patient operated upon for a dual-location tumour, and review of the literature.Results: The myxoma is a rare tumour. Various head and neck locations have been described, but not (to our knowledge) a tumour in both the oropharynx and the hypopharynx. Multiple synchronous locations must be searched for, particularly regarding cardiac myxoma.Conclusion: The myxoma is a rare, benign tumour, even rarer in the head and neck. Surgical treatment must be complete in order to avoid recurrences, and should be performed after assessment for cardiac involvement.
Improving Data Quality: Actors, Incentives, and Capabilities
Authors: Herrera Yoshiko M. , Kapur Devesh 
Published: April 2007

This paper examines the construction and use of data sets in political science. We focus on three interrelated questions: How might we assess data quality? What factors shape data quality? and How can these factors be addressed to improve data quality? We first outline some problems with existing data set quality, including issues of validity, coverage, and accuracy, and we discuss some ways of identifying problems as well as some consequences of data quality problems. The core of the paper addresses the second question by analyzing the incentives and capabilities facing four key actors in a data supply chain: respondents, data collection agencies (including state bureaucracies and private organizations), international organizations, and finally, academic scholars. We conclude by making some suggestions for improving the use and construction of data sets.It is a capital mistake, Watson, to theorise before you have all the evidence. It biases the judgment.—Sherlock Holmes in “A Study in Scarlet”Statistics make officials, and officials make statistics.”—Chinese proverb
“With Balanc't Air in Counterpoise”: Milton & Robert Boyle
Authors: Berkowitz M. S. 
Published: April 2007

Despite Kester Svendsen's otherwise authoritative study of Milton and science, his statement that Milton's “curiosity in science never advanced to the experiments of a Royal Society nor the speculations of a Descartes or a Hoboes”1 may now require some emendation. The evidence for this assertion appears in Book IV of Paradise Lost in the scene in which Gabriel and Satan stand ready to engage in what promises to be the world's first super‐heavyweight contest:Th’ Eternal to prevent such horrid fray Hung forth in Heav'n his golden Scales, yet seen Betwixt Astrea and the Scorpion sign, Wherein all things created first he weigh'd, The pendulous round Earth with balanc't Air in counterpoise ……2
ABSTRACTS
Authors: Cheney Margaret E. 
Published: April 2007

The following abstracts are from essays in Milton Studies 25 (1989), ed. James D. Simmonds. Pittsburgh, PA: U of Pittsburgh P, 1990.Stephen C. Behrendt. “Paradise Lost, History Painting, and Eighteenth‐Century English Nationalism.”Lloyd F. Dickson. “Against the Wiles of the Devil: Carlotta Petrina's Christocentric Illustrations of Paradise Lost.” 161–90.Steven C. Dillon. “Milton and the Poetics of Extremism.” 265–83.M. J. Doherty. “Salvation History, Poetic Form, and the Logic of Time in Milton's Nativity Ode.” 21–42.J. Karl Franson. “The Fatal Voyage of Edward King, Milton's Lycidas.” 43–67.John K. Hale. “Milton Playing with Ovid.” 3–19.Elizabeth Hanson. “To Smite Once and Yet Once More: The Transaction of Milton's Lycidas.” 69–88.Michael Lieb. “Reading God: Milton and the Anthropopathetic Tradition.” 213–43.Shirley Sharon‐Zisser. “Silence and Darkness in Paradise Lost.” 191–211.Keith W. F. Stavely. “Satan and Arminianism in Paradise Lost.” 125–39.Julia M. Walker. “Milton and Galileo: The Art of Intellectual Canonization.” 109–23.William Walker. “Typology and Paradise Lost, Books XI and XII.” 245–64.Robert Wiltenburg. “Damnation in a Roman Dress: Catiline, Catiline, and Paradise Lost.” 89–108.
Tidal Mixing in the Narrows of the Mersey Estuary
Authors: Hughes P. 
Published: April 2007

Summary
Observations of salinity in the Narrows of the River Mersey have shown that vertical mixing due to tidally induced turbulence may be complete at mid-tide. As tidal currents abate horizontal differential velocities, which constitute a seaward flow in the upper layer and an upriver flow near the bottom, become apparent and produce vertical salinity gradients. A second series of observations showed that vertical homogeneity may not be reached at any stage of the tide if the riverflow is high. Applying the theory for a vertically mixed estuary, coefficients of longitudinal eddy diffusion were computed for a low riverflow of 26 m3/s and gave a mean value of 160 m2/s. During a period of greater fresh water influx (103 m3/s) when conditions were less clearly defined, the average coefficient was considerably higher at 360 m2/s.