bluuebunny/crossref_metadata_2025_split huggingface dataset:
The hydrodynamic and conformational properties of denatured proteins in dilute solutions
Authors: Berry Guy C. 
Published: November 2009

AbstractPublished data on the characterization of unfolded proteins in dilute solutions in aqueous guanidine hydrochloride are analyzed to show that the data are not fit by either the random flight or wormlike chain models for linear chains. The analysis includes data on the intrinsic viscosity, root‐mean‐square radius of gyration, from small‐angle X‐ray scattering, and hydrodynamic radius, from the translational diffusion coefficient. It is concluded that residual structure consistent with that deduced from nuclear magnetic resonance on these solutions can explain the dilute solution results in a consistent manner through the presence of ring structures, which otherwise have an essentially flexible coil conformation. The ring structures could be in a state of continual flux and rearrangement. Calculation of the radius of gyration for the random‐flight model gives a similar reduction of this measure for chains joined at their endpoints, or those containing loop with two dangling ends, each one‐fourth the total length of the chain. This relative insensitivity to the details of the ring structure is taken to support the behavior observed across a range of proteins.
Laparoscopic subtotal hysterectomy versus laparoscopic total hysterectomy: a decade of experience
Authors: van Evert J. S. , Smeenk J. M. J. , Dijkhuizen F. P. H. L. J. , de Kruif J. H. , Kluivers K. B. 
Published: November 2009

AbstractAt present, there are only few data on the surgical outcomes of laparoscopic hysterectomy (LH). Up till now, it has been unclear whether there is a difference in number of complications among the subcategories of laparoscopic total hysterectomy and laparoscopic subtotal hysterectomy (LSH). Therefore, we have performed a retrospective analysis to evaluate the peri- and postoperative outcomes in women undergoing LSH versus LH. This multi-centre retrospective cohort study (Canadian Task Force classification II-2) was conducted in multi-centres (two teaching hospitals and one university medical centre) in the Netherlands, all experienced in minimally invasive gynaecology. In a multi-centre retrospective cohort study we compared the long-term outcomes of laparoscopic subtotal hysterectomy and laparoscopic total hysterectomy (including laparoscopic assisted vaginal hysterectomy, laparoscopic hysterectomy and total laparoscopic hysterectomy). All laparoscopic hysterectomies from the last 10 years (January 1998 till December 2007) were included. Patient characteristics, intra- and postoperative complications, operating time and duration of hospital stay were recorded. The minimum follow-up was 6 months. A total of 390 cases of laparoscopic hysterectomies were included in the analysis: 192 laparoscopic subtotal hysterectomies and 198 laparoscopic total hysterectomies. Patient characteristics such as age and parity were equal in the groups. The overall number of short-term and long-term complications was comparable in both groups: 17% and 15%. Short-term complications (bleeding, fever) were 3% in the LSH group and 12% in the LH group. Long-term complications were (tubal prolapse and cervical stump reoperations) 15% in the LSH group and 3% in the LH group. Laparoscopic subtotal hysterectomy as compared with the different types of laparoscopic total hysterectomy is associated with more long-term postoperative complications, whereas laparoscopic total hysterectomy is associated with more short-term complications.
Biomolecular Nano-Flow-Sensor to Measure Near-Surface Flow
Authors: Lee Sang-Wook , Kinoshita Haruyuki , Noji Hiroyuki , Fujii Teruo , Yamamoto Takatoki 
Published: November 2009

AbstractWe have proposed and experimentally demonstrated that the measurement of the near-surface flow at the interface between a liquid and solid using a 10 nm-sized biomolecular motor of F1-ATPase as a nano-flow-sensor. For this purpose, we developed a microfluidic test-bed chip to precisely control the liquid flow acting on the F1-ATPase. In order to visualize the rotation of F1-ATPase, several hundreds nanometer-sized particle was immobilized at the rotational axis of F1-ATPase to enhance the rotation to be detected by optical microscopy. The rotational motion of F1-ATPase, which was immobilized on an inner surface of the test-bed chip, was measured to obtain the correlation between the near-surface flow and the rotation speed of F1-ATPase. As a result, we obtained the relationship that the rotation speed of F1-ATPase was linearly decelerated with increasing flow velocity. The mechanism of the correlation between the rotation speed and the near-surface flow remains unclear, however the concept to use biomolecule as a nano-flow-sensor was proofed successfully.(See supplementary material 1)
New Bending Algorithm for Field-Driven Molecular Dynamics
Authors: Chen Dao-Long , Chen Tei-Chen , Lai Yi-Shao 
Published: November 2009

Abstract
A field-driven bending method is introduced in this paper according to the coordinate transformation between straight and curved coordinates. This novel method can incorporate with the periodic boundary conditions in analysis along axial, bending, and transverse directions. For the case of small bending, the bending strain can be compatible with the beam theory. Consequently, it can be regarded as a generalized SLLOD algorithm. In this work, the bulk copper beam under bending is analyzed first by the novel bending method. The bending stress estimated here is well consistent to the results predicted by the beam theory. Moreover, a hollow nanowire is also analyzed. The zigzag traces of atomic stress and the corresponding 422 common neighbor type can be observed near the inner surface of the hollow nanowire, which values are increased with an increase of time. It can be seen that the novel bending method with periodic boundary condition along axial direction can provide a more physical significance than the traditional method with fixed boundary condition.
Photovoltaic Properties of p-Doped GaAs Nanowire Arrays Grown on n-Type GaAs(111)B Substrate
Authors: Cirlin G. E. , Bouravleuv A. D. , Soshnikov I. P. , Samsonenko Yu B. , Dubrovskii V. G. , Arakcheeva E. M. , Tanklevskaya E. M. , Werner P. 
Published: November 2009

Abstract
We report on the molecular beam epitaxy growth of Au-assisted GaAs p-type-doped NW arrays on the n-type GaAs(111)B substrate and their photovoltaic properties. The samples are grown at different substrate temperature within the range from 520 to 580 °C. It is shown that the dependence of conversion efficiency on the substrate temperature has a maximum at the substrate temperature of 550 °C. For the best sample, the conversion efficiency of 1.65% and the fill factor of 25% are obtained.
Comparing Process Efficiency in Reducing Steryl Glucosides in Biodiesel
Authors: Tang Haiying , De Guzman Rhet , Salley Steven , Ng K. Y. Simon 
Published: November 2009

AbstractA significant obstacle to the commercial acceptance of biodiesel is the potential for filter plugging due to precipitates in the fuel. The majority of these precipitates can be attributed to either steryl glucosides (SGs) or monoacylglycerols in biodiesel. A GC–FID method to quantify minor components content in biodiesel is presented. The effectiveness of room temperature and cold soak filtration, adsorbent treatment, centrifuge, and vacuum distillation processes for SG removal was studied. The vacuum distillation process is the most effective method of removing the SG from biodiesel.
Connective tissue growth factor is induced in bleomycin‐induced skin scleroderma
Authors: Liu Shangxi , Taghavi Reza , Leask Andrew 
Published: November 2009

AbstractThe origin of fibrotic cells within connective tissue is unclear. For example, the extent to which microvascular pericytes contribute to the number of myofibroblasts present in dermal fibrosis in uncertain. Connective tissue growth factor (CTGF/CCN2) is a marker and mediator of fibrosis. In this report, we use an antibody recognizing CCN2 to assess the cell types in mouse dermis which express CCN2 in the bleomycin model of skin scleroderma. Control (PBS injected) and fibrotic (bleomycin‐injected) dermis was examined for CCN2, α‐smooth muscle actin (α‐SMA) (to detect myofibroblasts), and NG2 (to detect pericytes) expression. Consistent with previously published data, CCN2 expression was largely absent in the dermis of control mice. However, upon exposure to bleomycin, CCN2 was observed in the dermis. Cells that expressed CCN2 were α−SMA‐expressing myofibroblasts. Approximately 85% of myofibroblasts were NG2‐positive, CCN2‐expressing pericytes, indicating that pericytes significantly contributed to the presence of myofibroblasts in sclerotic dermis. Thus CCN2 is induced in fibrotic skin, correlating with the induction of myofibroblast induction. Moreover, CCN2‐expressing pericytes significantly contribute to the appearance of myofibroblasts in bleomycin‐induced skin scleroderma.
Pollen–pistil interaction, pistil histology and seed production in A×B grain sorghum crosses under chilling field temperatures
Authors: CISNEROS-LÓPEZ M. E. , MENDOZA-ONOFRE L. E. , ZAVALETA-MANCERA H. A. , GONZÁLEZ-HERNÁNDEZ V. A. , MORA-AGUILERA G. , CÓRDOVA-TÉLLEZ L. , HERNÁNDEZ-MARTÍNEZ M. 
Published: November 2009

SUMMARYSix pairs of isogenic lines of sorghum (Sorghum bicolor L. Moench) were sown in field plots in Montecillo, State of México (2240 m altitude), in 2005 and 2006. Crosses A (♀)×B (♂) were done in each pair. In A-lines, the length of pistil, stigma, style and ovary, as well as the ovary width, were measured. In B-lines, pollen diameter, viability (cytoplasm density) and production were evaluated. Pollen germination and pollen tube growth in the pistils of the A-lines, were quantified in vivo with aniline blue and epifluorescence 18 h after pollination (HAP), while fertilized pistils were counted at 96 HAP. Histological studies on both pollinated and non-pollinated pistils were performed in one male-sterile line. Seed yield, mean-seed weight, seeds per panicle and seed set (SS; seeds/flower/panicle) were determined at harvest. Pollen viability was the variable most related to pollen germination and pollen tube growth. Stigma receptivity was not associated with its morphology. Growth of the pollen tube in stigma, style and ovary was observed in the transmitting tissue 18 HAP, running parallel to the vascular tissue. Yield under chilling field temperatures (minimum average of 6 and 8°C) prevailing during flower development and pollination ranged from 7 to 12 g/panicle. The differences in seed production and SS among A×B crosses did not depend on the amount and viability of pollen.
Graph Partitioning via Adaptive Spectral Techniques
Authors: COJA-OGHLAN AMIN 
Published: November 2009

In this paper we study the use of spectral techniques for graph partitioning. Let G = (V, E) be a graph whose vertex set has a ‘latent’ partition V1,. . ., Vk. Moreover, consider a ‘density matrix’ Ɛ = (Ɛvw)v, sw∈V such that, for v ∈ Vi and w ∈ Vj, the entry Ɛvw is the fraction of all possible Vi−Vj-edges that are actually present in G. We show that on input (G, k) the partition V1,. . ., Vk can (very nearly) be recovered in polynomial time via spectral methods, provided that the following holds: Ɛ approximates the adjacency matrix of G in the operator norm, for vertices v ∈ Vi, w ∈ Vj ≠ Vi the corresponding column vectors Ɛv, Ɛw are separated, and G is sufficiently ‘regular’ with respect to the matrix Ɛ. This result in particular applies to sparse graphs with bounded average degree as n = #V → ∞, and it has various consequences on partitioning random graphs.
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
Authors: Robinson Mark D. , McCarthy Davis J. , Smyth Gordon K. 
Published: November 2009

AbstractSummary: It is expected that emerging digital gene expression (DGE) technologies will overtake microarray technologies in the near future for many functional genomics applications. One of the fundamental data analysis tasks, especially for gene expression studies, involves determining whether there is evidence that counts for a transcript or exon are significantly different across experimental conditions. edgeR is a Bioconductor software package for examining differential expression of replicated count data. An overdispersed Poisson model is used to account for both biological and technical variability. Empirical Bayes methods are used to moderate the degree of overdispersion across transcripts, improving the reliability of inference. The methodology can be used even with the most minimal levels of replication, provided at least one phenotype or experimental condition is replicated. The software may have other applications beyond sequencing data, such as proteome peptide count data.Availability: The package is freely available under the LGPL licence from the Bioconductor web site (http://bioconductor.org).Contact: mrobinson@wehi.edu.au
Co-expression networks: graph properties and topological comparisons
Authors: Xulvi-Brunet Ramon , Li Hongzhe 
Published: November 2009

Abstract
Motivation: Microarray-based gene expression data have been generated widely to study different biological processes and systems. Gene co-expression networks are often used to extract information about groups of genes that are ‘functionally’ related or co-regulated. However, the structural properties of such co-expression networks have not been rigorously studied and fully compared with known biological networks. In this article, we aim at investigating the structural properties of co-expression networks inferred for the species Saccharomyces Cerevisiae and comparing them with the topological properties of the known, well-established transcriptional network, MIPS physical network and protein–protein interaction (PPI) network of yeast.
Results: These topological comparisons indicate that co-expression networks are not distinctly related with either the PPI or the MIPS physical interaction networks, showing important structural differences between them. When focusing on a more literal comparison, vertex by vertex and edge by edge, the conclusion is the same: the fact that two genes exhibit a high gene expression correlation degree does not seem to obviously correlate with the existence of a physical binding between the proteins produced by these genes or the existence of a MIPS physical interaction between the genes. The comparison of the yeast regulatory network with inferred yeast co-expression networks would suggest, however, that they could somehow be related.
Conclusions: We conclude that the gene expression-based co-expression networks reflect more on the gene regulatory networks but less on the PPI or MIPS physical interaction networks.
Contact: hongzhe@mail.med.upenn.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Identification of substrates for Ser/Thr kinases using residue-based statistical pair potentials
Authors: Kumar Narendra , Mohanty Debasisa 
Published: November 2009

Abstract
Motivation: In silico methods are being widely used for identifying substrates for various kinases and deciphering cell signaling networks. However, most of the available phosphorylation site prediction methods use motifs or profiles derived from a known data set of kinase substrates and hence, their applicability is limited to only those kinase families for which experimental substrate data is available. This prompted us to develop a novel multi-scale structure-based approach which does not require training using experimental substrate data.
Results:In this work, for the first time, we have used residue-based statistical pair potentials for scoring the binding energy of various substrate peptides in complex with kinases. Extensive benchmarking on Phospho.ELM data set indicate that our method outperforms other structure-based methods and has a prediction accuracy comparable to available sequence-based methods. We also demonstrate that the rank of the true substrate can be further improved, if the high-scoring candidate substrates that are short-listed based on pair potential score, are modeled using all atom forcefield and MM/PBSA approach.
Contact: deb@nii.res.in
Supplementary information: Supplementary data are available at Bioinformatics Online.
PerturbationAnalyzer: a tool for investigating the effects of concentration perturbation on protein interaction networks
Authors: Li Fei , Li Peng , Xu Wenjian , Peng Yuxing , Bo Xiaochen , Wang Shengqi 
Published: November 2009

Abstract
Summary:The propagation of perturbations in protein concentration through a protein interaction network (PIN) can shed light on network dynamics and function. In order to facilitate this type of study, PerturbationAnalyzer, which is an open source plugin for Cytoscape, has been developed. PerturbationAnalyzer can be used in manual mode for simulating user-defined perturbations, as well as in batch mode for evaluating network robustness and identifying significant proteins that cause large propagation effects in the PINs when their concentrations are perturbed. Results from PerturbationAnalyzer can be represented in an intuitive and customizable way and can also be exported for further exploration. PerturbationAnalyzer has great potential in mining the design principles of protein networks, and may be a useful tool for identifying drug targets.
Availability:PerturbationAnalyzer can be accessed from the Cytoscape web site http://www.cytoscape.org/plugins/index.php or http://biotech.bmi.ac.cn/PerturbationAnalyzer.
Contact: boxc@bmi.ac.cn; sqwang@bmi.ac.cn
Supplementary information: Supplementary data are available at Bioinformatics online.
PyNAST: a flexible tool for aligning sequences to a template alignment
Authors: Caporaso J. Gregory , Bittinger Kyle , Bushman Frederic D. , DeSantis Todd Z. , Andersen Gary L. , Knight Rob 
Published: November 2009

Abstract
Motivation: The Nearest Alignment Space Termination (NAST) tool is commonly used in sequence-based microbial ecology community analysis, but due to the limited portability of the original implementation, it has not been as widely adopted as possible. Python Nearest Alignment Space Termination (PyNAST) is a complete reimplementation of NAST, which includes three convenient interfaces: a Mac OS X GUI, a command-line interface and a simple application programming interface (API).
Results: The availability of PyNAST will make the popular NAST algorithm more portable and thereby applicable to datasets orders of magnitude larger by allowing users to install PyNAST on their own hardware. Additionally because users can align to arbitrary template alignments, a feature not available via the original NAST web interface, the NAST algorithm will be readily applicable to novel tasks outside of microbial community analysis.
Availability: PyNAST is available at http://pynast.sourceforge.net.
Contact: rob.knight@colorado.edu
The analysis of echotrace obtained by a split-beam echosounder to observe the tilt-angle dependence of fish target strength in situ
Authors: Furusawa Masahiko , Amakasu Kazuo 
Published: November 2009

Abstract
Furusawa, M., and Amakusu, K. 2010. The analysis of echotrace obtained by a split-beam echosounder to observe the tilt-angle dependence of fish target strength in situ. – ICES Journal of Marine Science, 67: 215–230. A method of echotrace analysis (ETA), proposed by Furusawa and Miyanohana in 1988 utilizes successive echodata from an individual fish to obtain the target-strength (TS) pattern as a function of fish tilt angle and behaviour. The method can be applied to data from an echosounder with any beam configuration, single-, dual-, and split-beam. However, the method has not been applied rigorously to split-beam sounder data, which provide most comprehensive and accurate information. The aim of this work is to establish an accurate and practical ETA method for split-beam echosounder data. Although the basic theory had already been developed, some theoretical and practical enhancement was needed; smoothing of an echotrack by linear and quadratic regressions, correction for transducer motion, and comparison of an observed TS pattern with a prolate-spheroid theoretical model. The analysis starts from careful selection of a single echotrace on an echogram and ends with a composite display of results including a three-dimensional fish track and a TS pattern as a function of the tilt angle of the fish. The method was applied to typical echotrace examples, and utility and practicality were confirmed. A means of increasing the number of applicable echotraces is discussed.
Remote sensing of underwater vegetation using single-beam acoustics
Authors: Quintino Victor , Freitas Rosa , Mamede Renato , Ricardo Fernando , Rodrigues Ana Maria , Mota Jorge , Pérez-Ruzafa Ángel , Marcos Concepción 
Published: November 2009

Abstract
Quintino, V., Freitas, R., Mamede, R., Ricardo, F., Rodrigues, A. M., Mota, J., Pérez-Ruzafa, Á., and Marcos, C. 2010. Remote sensing of underwater vegetation using single-beam acoustics. – ICES Journal of Marine Science, 67: 594–605. A single-beam, acoustic, ground-discrimination system (QTC VIEW, Series V) was used to study the distribution of underwater macrophytes in a shallow-water coastal system, employing frequencies of 50 and 200 kHz. The study was conducted in Mar Menor, SE Spain, where the expansion of Caulerpa prolifera has contributed to the silting up of the superficial sediments. A direct relationship was identified between algal biomass and sediment-fines content. Acoustic information on sediment grain size and data on algal biomass were obtained in muddy and sandy sediments, including vegetated and non-vegetated seabed. Non-vegetated muddy areas were created by diving and handpicking the algae. The multivariate acoustic data were analysed under the null hypotheses that there were no acoustic differences between bare seabeds with contrasting superficial sediment types or among low, medium, and high algal-biomass areas, having in mind that grain size can act as a confounding factor. Both null hypotheses were rejected, and the results showed that 200 kHz was better than 50 kHz in distinguishing cover levels of algal biomass. The relationship between the 200-kHz acoustic data and algal biomass suggests utility in modelling the latter using the former.
Immediate maximum economic yield; a realistic fisheries economic reference point
Authors: Lleonart Jordi , Merino Gorka 
Published: November 2009

Abstract
Lleonart, J., and Merino, G. 2010. Immediate maximum economic yield; a realistic fisheries economic reference point. – ICES Journal of Marine Science, 67: 577–582. Unregulated or poorly managed fisheries tend towards overexploitation, but fisheries rent does not completely dissipate when immediate rent maximization is sought. The principle of immediate economic rent maximization is the basis of the derivation of a classic model and has led to the definition of a relationship in a catch-and-effort diagram termed the dynamic immediate maximum economic yield (DIMEY) curve. For any initial biomass, if the economic rent in the immediate fishing season is maximized, then the fishing effort and catch strategy that follows will be located on the DIMEY curve. The DIMEY curve is not only used for dynamic simulation but also used to identify a new reference point, the immediate maximum economic yield (IMEY), which is proposed as more realistic than the classic open-access solution for unregulated fisheries. IMEY is proposed as an asymptotic outcome for unregulated or poorly managed fisheries when short-term economic objectives drive fleet activities. IMEY properties are described and compared with traditional fisheries reference points in the yield-and-effort diagram. Theoretical conclusions are compared with empirical evidence provided by the red shrimp fishery off Blanes, Spain (NW Mediterranean). Observed catch-and-effort records are plotted and were positively correlated with the DIMEY curve and IMEY.