bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis and prediction of calcium‐binding pockets from apo‐protein structures exhibiting calcium‐induced localized conformational changes
Authors: Wang Xue , Zhao Kun , Kirberger Michael , Wong Hing , Chen Guantao , Yang Jenny J. 
Published: March 2010

AbstractCalcium binding in proteins exhibits a wide range of polygonal geometries that relate directly to an equally diverse set of biological functions. The binding process stabilizes protein structures and typically results in local conformational change and/or global restructuring of the backbone. Previously, we established the MUG program, which utilized multiple geometries in the Ca2+‐binding pockets of holoproteins to identify such pockets, ignoring possible Ca2+‐induced conformational change. In this article, we first report our progress in the analysis of Ca2+‐induced conformational changes followed by improved prediction of Ca2+‐binding sites in the large group of Ca2+‐binding proteins that exhibit only localized conformational changes. The MUGSR algorithm was devised to incorporate side chain torsional rotation as a predictor. The output from MUGSR presents groups of residues where each group, typically containing two to five residues, is a potential binding pocket. MUGSR was applied to both X‐ray apo structures and NMR holo structures, which did not use calcium distance constraints in structure calculations. Predicted pockets were validated by comparison with homologous holo structures. Defining a “correct hit” as a group of residues containing at least two true ligand residues, the sensitivity was at least 90%; whereas for a “correct hit” defined as a group of residues containing at least three true ligand residues, the sensitivity was at least 78%. These data suggest that Ca2+‐binding pockets are at least partially prepositioned to chelate the ion in the apo form of the protein.
Effect of acetic acid on CO2 corrosion of carbon steel in NaCl solution
Authors: Yin Z. F. , Bai Z. Q. , Zhou W. J. , Li Bin 
Published: March 2010

AbstractPotentiodynamic sweep and electrochemical impedance spectroscopy measurements were applied to investigate the effects of both temperature and acetic acid (HAc) on the anodic and cathodic reactions in CO2 corrosion of P110 steel in 3.5% NaCl solution. The temperatures were controlled at 30 and 60 °C. The concentrations of HAc were controlled at 0, 1000, 3000 and 5000 ppm. In this work, the corrosion parameters of polarization curves, such as corrosion potential (Ecorr), corrosion current density (icorr), and anodic and cathodic branch slopes (ba and bc), are presented and discussed in detail. In addition, the equivalent circuit models and ZsimpWin software were utilized to discuss the Nyquist plots. The plots showed that the Ecorr values shifted in the positive direction as the HAc concentration increased. The icorr values increased with the increase in HAc concentration, indicating that HAc could accelerate the corrosion. The impedance spectra measured at 30 and 60 °C have different time constants and characterization. The coverage fraction θ and the thickness L of corrosion film are two most important controlled variables that influence and control the CO2 corrosion mechanisms. Copyright © 2010 John Wiley & Sons, Ltd.
Distribution of inkjet ink components via ToF‐SIMS imaging
Authors: Filenkova A. , Acosta E. , Brodersen P. M. , Sodhi R. N. S. , Farnood R. 
Published: March 2010

AbstractTo optimize the performance of the inkjet printing process it is of significant importance to have greater understanding of the spatial arrangement of not only ink colourant, but also other ink components such as surfactant, solvent and/or cosolvent. In this work, the capabilities of Time‐of‐Flight (ToF) SIMS are applied to study the spreading (xy distribution) of a custom inkjet ink formulation, containing cationic crystal violet dye, ethoxylated surfactant and ink vehicle/solvent marked by lithium salt on uncoated and coated papers. High spatially resolved images obtained by ToF‐SIMS clearly illustrate differentiation of individual ink components, with irregular spreading on uncoated paper leading to poor edge definition, and as a result, poor print quality. ToF‐SIMS images and distribution profiles of ink components on ‘best’ and ‘worst’ commercial paper samples show that the cationic dye is preferentially adsorbed by both substrates, colocalizing with the surfactant. However, the solvent, marked by lithium salt, spreads 20% more than cationic dye on coated paper, and 25% more than the dye on uncoated paper. The variability in preferential absorption of ink components due to morphology, chemistry and topography of paper, may be taken as an indication of print quality. Copyright © 2010 John Wiley & Sons, Ltd.
Unilateral coronal diameters of the levator hiatus: baseline data for the automated detection of avulsion of the levator ani muscle
Authors: Ismail S. I. M. F. , Shek K. L. , Dietz H. P. 
Published: March 2010

AbstractObjectiveLevator ani avulsion injury is associated with pelvic organ prolapse. Although it can be detected by magnetic resonance imaging or translabial ultrasonography, both require substantial training. This retrospective study provides baseline measurements of the unilateral coronal or transverse diameter of the levator hiatus and assesses its use in the prediction of levator ani avulsion injury, as a step towards automated detection.MethodsDatasets of 787 patients seen in a tertiary urogynecological unit were assessed, including history, examination and three/four‐dimensional pelvic floor ultrasound. Unilateral coronal diameters were measured off‐line in stored volume datasets, with the operator blinded to clinical data. Volumes obtained during maximum pelvic floor muscle contraction were used, resorting to volumes obtained at rest for patients unable to contract their pelvic floor muscles.ResultsUltrasound images were available for 761 patients, including 16 (2.1%) who could not contract their pelvic floor muscles, generating 1522 unilateral measurements (both sides for 761 patients). Levator ani avulsion injury was associated with significant increase in the unilateral coronal diameter (2.57 ± 0.5 vs. 2.1 ± 0.3 cm, P < 0.0001). Receiver–operating characteristics curve analysis showed an area under the curve of 0.801 (95% CI, 0.765–0.837). A cut‐off of 2.3 cm had a sensitivity of 71% and a specificity of 79% for the diagnosis of levator ani avulsion injury.ConclusionsLevator ani avulsion injury is associated with a significant increase in unilateral coronal diameter, a cut‐off point of 2.3 cm being most appropriate for alerting clinicians to a high likelihood of this diagnosis. It is hoped that this information will help to automate the detection of levator ani avulsion injury. Copyright © 2010 ISUOG. Published by John Wiley & Sons, Ltd.
Activity pattern, reproductive behaviors and gonadal hormones in the raccoon dog (Nyctereutes procyonoides)
Authors: Rudert S. , Brown J.L. , Gansloßer U. , Möbius G. , Songsasen N. 
Published: March 2010

AbstractThe objectives of this study were to (1) assess year‐round behaviors and activity patterns of captive raccoon dogs (Nyctereutes procyonoides) and (2) characterize the species' reproductive endocrinology. Behaviors and activity patterns of 12 (5.7) animals were recorded over a 1‐year period. During that time, fecal samples were collected 2–7 times/week from 16 (7.9) individuals (six of these were included in the behavioral study) for the analysis of testosterone, progesterone and estrogen metabolite concentrations. Activity pattern and excretion of gonadal steroids followed a seasonal pattern. Specifically, dogs were cathemeral in summer, and primarily nocturnal in winter. In the males, testosterone concentrations were at baseline from April through September, began to rise in October and reached peak concentrations in February (P<0.05). In the females, elevated estrogen (P<0.05) was observed in March followed by an increase in progestagen concentrations from March through May (P<0.05) in both pregnant and pseudopregnant animals. Gender significantly influenced monthly testosterone/estrogen ratio (P<0.01); values were higher in males than in females throughout the year with overall percentage of overlapping values between males and females being 28%. In summary, this study characterized cirannual fluctuations in behaviors and gonadal steroid metabolites in the raccoon dog maintained in captivity. Because there is no obvious sexual dimorphism, the differences in testosterone/estrogen ratio may be useful for gender differentiation (72% accuracy), especially among individuals living in the wild. Zoo Biol 30:134–148, 2011. © 2010 Wiley‐Liss, Inc.
Entrapment of Flaxseed Oil Within Gelatin‐Gum Arabic Capsules
Authors: Liu S. , Low N. H. , Nickerson Michael T. 
Published: March 2010

AbstractThe aim of this study was to optimize the encapsulation of flaxseed oil within a gelatin‐gum Arabic (GA) matrix via complex coacervation. The effect of homogenization rates (3,000–15,000 rpm) and total biopolymer concentrations (1–2% w/v) on emulsion efficiency was studied in order to optimize the wall matrix. The physicochemical properties of the dried powder, and the capsule's ability to inhibit oxidation during storage were assessed. As homogenization rates increased from 3,000 to 9,000 rpm, the structure of the capsule transitioned from a spherical mononuclear‐type to irregular‐shaped multinuclear capsules. The size of the capsules and amount of non‐encapsulated oil was found to increase as the total biopolymer concentration was raised from 1 to 2% (w/v). Subsequently, gelatin‐GA capsules were produced with a 1:1 core‐to‐wall ratio at a total biopolymer concentration of 2% (w/v) and at a homogenization rate of 9,000 rpm. Formed capsules had an encapsulation efficiency of 84% and showed a protective effect against the production of primary and secondary oxidative products versus non‐encapsulated oil during 25 days of room temperature storage.
Bone mineral density in women of a low socioeconomic level using DMPA for contraception in rural Upper Egypt
Authors: Hussein Mostafa , Mahran Dalia G. , Farouk Osama A. , El‐Assal Maher A. , Fathallah Mohammad M. , Romih Mahmoud S. 
Published: March 2010

AbstractObjectiveTo evaluate the effect of long‐term use of depot medroxyprogesterone acetate (DMPA) on bone mineral density (BMD).MethodsA cross‐sectional study was performed with 150 women using DMPA and 136 women using nonhormonal methods of contraception in rural Sohag Governorate, Upper Egypt. Socioeconomic scores were measured using the 1983 Fahmy and El Sherbeny system, model II. The mineral density of the left calcaneus was measured by ultrasonographically.ResultsIf the overall mean T score was significantly lower for the DMPA than for the control group, osteopenia and osteoporosis were more prevalent among DMPA users only for participants of the lowest socioeconomic level. There was a mild negative correlation between duration of DMPA use and T score, and when contraception duration was considered the differences in T scores between the DMPA and control groups were significant.ConclusionPrescribing DMPA only for the short term to women of a low socioeconomic level and counseling them about its effect on bone density may be a practical approach.
Induction of labor with vaginal misoprostol plus oxytocin versus oxytocin alone
Authors: Balci Osman , Mahmoud Alaa S. , Ozdemir Suna , Acar Ali 
Published: March 2010

AbstractObjectiveTo compare the effect of an oxytocin infusion alone or preceded by an intravaginal application of misoprostol for labor induction in women with term pregnancies and a low Bishop score.MethodsThis study randomized 100 multiparous women with singleton pregnancies over 38 weeks and a Bishop score less than 6 to receive either a single 50‐µg dose of misoprostol intravaginally 3 hours before initiation of the oxytocin infusion or only an oxytocin infusion. The time from induction to delivery, the route of delivery, and maternal and fetal outcomes were analyzed.ResultsThe mean time from induction to delivery was 9.36 ± 1.97 hours in the misoprostol plus oxytocin group and 11.08 ± 3.23 in the oxytocin alone group (P = 0.002). The rates of vaginal delivery, 1‐ and 5‐minute Agpar scores, placental abruption, and postpartum hemorrhage were similar between the 2 groups, as were the rates of admission to the neonatal intensive care unit. There were no cases of perinatal asphyxia.ConclusionA 50‐µg intravaginal application of misoprostol before starting the oxytocin infusion is a more effective method of labor induction than an oxytocin infusion alone for our study population.
Assessing the use and weight of information and evidence in U.S. state policy decisions
Authors: Hall Jeremy L , Jennings Edward T 
Published: March 2010

Abstract
This study reports results from a 2008 survey of U.S. State agency administrators across all 50 states and 12 different agency types. Agency managers were asked to disclose the extent to which they relied on information from 19 information sources and to weight the value of information from each source. This paper is particularly interested in ascertaining the proportion of agency policies that are based on formal scientific evidence, and the importance of scientific information as a source of influence on agency decisions relative to other potential sources of information. Information is presented by agency type with significant differences across substantive policy areas noted. Using a weighted index approach, we combine the frequency of consultation of an information source with the weight placed on that evidence by the agency administrator in developing programs and practices. Using these weighted scores, we further examine the relationship of these responses to the weight agencies place on information from various sources.
Mammal and insect predation of chemically and structurally defended Mucuna holtonii (Fabaceae) seeds in a Costa Rican rain forest
Authors: Kuprewicz Erin K. , García-Robledo Carlos 
Published: March 2010

Abstract:To prevent seed losses from predation, plants have developed protective strategies. Seeds may utilize chemical or structural defences to deter predators. Mucuna holtonii (Fabaceae) has large seeds containing a toxic amino acid, L-dopa, and covered with a hard seed coat. Our study assessed the effectiveness of chemical and mechanical seed defences against vertebrate and invertebrate seed predators within Estación Biológica La Selva, Costa Rica. Pre-dispersal insect and fungus attack of M. holtonii seeds was low (95.7% of 1493 seeds were undamaged). Camera traps monitoring 90 marked M. holtonii seeds showed that the collared peccary (Pecari tajacu) consumed 98.6% of 69 removed seeds over 16 d. Field experiments involving 100 seeds with intact and 100 with opened seed coats found that only opened seeds had endosperm removed by Sericomyrmex amabilis ants (0.5–100% of endosperm removed). Shade-house experiments showed that seeds with high amounts of endosperm removed by ants resulted in low germination success and low seedling biomass production. Although M. holtonii seeds are rich in L-dopa, this compound is not an effective chemical defence against mammals that possess foregut fermentation. The seed coat of M. holtonii is an effective structural defence against invertebrate seed predators, preventing endosperm removal and enhancing seedling survival.
Building a high-quality sense inventory for improved abbreviation disambiguation
Authors: Okazaki Naoaki , Ananiadou Sophia , Tsujii Jun'ichi 
Published: March 2010

Abstract
Motivation: The ultimate goal of abbreviation management is to disambiguate every occurrence of an abbreviation into its expanded form (concept or sense). To collect expanded forms for abbreviations, previous studies have recognized abbreviations and their expanded forms in parenthetical expressions of bio-medical texts. However, expanded forms extracted by abbreviation recognition are mixtures of concepts/senses and their term variations. Consequently, a list of expanded forms should be structured into a sense inventory, which provides possible concepts or senses for abbreviation disambiguation.
Results: A sense inventory is a key to robust management of abbreviations. Therefore, we present a supervised approach for clustering expanded forms. The experimental result reports 0.915 F1 score in clustering expanded forms. We then investigate the possibility of conflicts of protein and gene names with abbreviations. Finally, an experiment of abbreviation disambiguation on the sense inventory yielded 0.984 accuracy and 0.986 F1 score using the dataset obtained from MEDLINE abstracts.
Availability: The sense inventory and disambiguator of abbreviations are accessible at http://www.nactem.ac.uk/software/acromine/ and http://www.nactem.ac.uk/software/acromine_disambiguation/
Contact: okazaki@chokkan.org
DistanceScan: a tool for promoter modeling
Authors: Shelest Vladimir , Albrecht Daniela , Shelest Ekaterina 
Published: March 2010

Abstract
Summary: The state of the art in promoter modeling for higher eukaryotes is predicting not single transcription factor binding sites (TFBSs), but their combinations. The new tool utilizes a previously developed method of distance distributions of TFBS pairs. We model the random distribution of distances and compare it with the distribution observed in the query sequences. Comparison of the profiles allows filtering out the ‘noise’ and retaining the potentially functional combinations. This approach has proved its usefulness as a filtering technique for the selection of TFBS pairs for promoter modeling and is now implemented as a tool in R. As an input, it can use the outputs of three different TFBS- and motif-predictive tools (Gibbs Sampler for motifs, MatchTM and MEME/FIMO for PWM-based search). The output is a list of predicted pairs on overrepresented distances with assigned scores, P-values and plots showing the distribution of pairs in the input sequences.
Availability: The tool is available at https://www.omnifung.hki-jena.de/Rpad/Distance_Scan/index.htm
Contact: ekaterina.shelest@hki.jena.de
Supplementary information: Supplementary Data are available at Bioinformatics online.
Does DNA extraction affect the physical and chemical composition of historical cod (Gadus morhua) otoliths?
Authors: Therkildsen Nina Overgaard , Nielsen Einar Eg , Hüssy Karin , Meldrup Dorte , Geffen Audrey J. 
Published: March 2010

Abstract
Therkildsen, N. O., Nielsen, E. E., Hüssy, K., Meldrup, D., and Geffen, A. J. 2010. Does DNA extraction affect the physical and chemical composition of historical cod (Gadus morhua) otoliths? – ICES Journal of Marine Science, 67: 1251–1259. Archived otoliths constitute an important source of historical DNA for use in temporal genetic studies, but such otoliths are also valuable for other research applications, e.g. growth or microchemistry studies, where information about the past is of relevance. Consequently, there are potentially conflicting interests regarding how the limited and irreplaceable otolith collections should be used. To resolve this, it is important to find out whether DNA extraction damages otoliths such that they can no longer be used for other research purposes or whether individual otoliths can be used in multiple applications. We examined the effects of three different DNA extraction methods on the elemental composition, the morphology, and the clarity of annual growth increments for successful age estimation of Atlantic cod (Gadus morhua) otoliths that had been archived for 0–31 years. The three extraction methods yielded DNA of comparable quality, and none of the methods caused major damage to the otoliths. Of the element concentrations measured, only Mg and Rb showed considerable changes resulting from DNA extraction. The physical properties of the otolith (morphology and clarity of annual growth increments) were not affected. Hence, cod otoliths can be used for several research purposes after DNA extraction.
Age-based demography and reproduction of hapuku, Polyprion oxygeneios, from the south coast of Western Australia: implications for management
Authors: Wakefield Corey B. , Newman Stephen J. , Molony Brett W. 
Published: March 2010

Abstract
Wakefield, C. B., Newman, S. J., and Molony, B. W. 2010. Age-based demography and reproduction of hapuku, Polyprion oxygeneios, from the south coast of Western Australia: implications for management. – ICES Journal of Marine Science, 67: 1164–1174. The hapuku, Polyprion oxygeneios, inhabits deep (>100 m) continental slope waters of Western Australia. In all, 1352 P. oxygeneios were collected from the waters along the south coast of Western Australia (ca. 35°S) from 2004 to 2008. The species is gonochoristic, and spawns during the austral winter (May–September). Ages were estimated from counts of opaque zones from thin-sectioned sagittal otoliths. Classification analysis of the outer margin of sectioned otoliths indicated that a single opaque zone is deposited annually. Female P. oxygeneios (n = 630; 535–1114 mm total length, TL) ranged in age from 2 to 35 years and males (n = 691; 521–1004 mm TL) from 2 to 52 years. von Bertalanffy growth models for male and female P. oxygeneios were statistically, but not biologically, different (<5% difference in mean and estimated lengths-at-age). Estimates of the lengths and ages at which 50% of the females and males in the population reached sexual maturity were 760 and 702 mm TL and 7.1 and 6.8 years. The instantaneous rate of natural mortality (M) was estimated to be 0.09. Estimates of the instantaneous rate of fishing mortality (F) were low (0.01–0.05). Harvest rates in 2005 and 2006 were close to estimated sustainable levels. Monitoring of any future increases in catch and effort in continental slope waters in both State- and Commonwealth-managed fisheries is required in order to assess impacts to stock sustainability. Sustainable management would also benefit from improved understanding of possible pan-oceanic recruitment of the species among southern hemisphere populations.
Potato Zebra Chip Disease: A Phytopathological Tale
Authors: Crosslin James M. , Munyaneza Joseph E. , Brown Judith K. , Liefting Lia W. 
Published: March 2010

Potato zebra chip (ZC) disease is a relative newcomer to the world of important potato diseases. First reported in Mexico in the 1990s, by 2004-2005 the disease was causing serious economic damage in parts of Texas. ZC is now widespread in the south-western and central United States, Mexico, Central America, and was recently reported in New Zealand. By 2006, there seemed to be an association between ZC and the potato psyllid (Bactericera cockerelli). The exact nature of the relationship, however, has only recently been identified by the discovery of a new Candidatus Liberibacter bacterium that is transmitted to potatoes, tomatoes, and other solanaceous hosts by the potato psyllid. This review examines the history of this disease, the association of ZC with the potato psyllid, the host range, and recent research into the bacterial pathogen. Accepted for publication 15 December 2009. Published 17 March 2010.