bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Tool and Index to Assess Surgical Capacity in Low Income Countries: An Initial Implementation in Sierra Leone
Authors: Groen Reinou S. , Kamara Thaim B. , Dixon‐Cole Richmond , Kwon Steven , Kingham T. Peter , Kushner Adam L. 
Published: April 2012

AbstractBackgroundA first step toward improving surgical care in many low and middle income countries is to document the need. To facilitate the collection and analysis of surgical capacity data and measure changes over time, Surgeons OverSeas (SOS) developed a tool and index based on personnel, infrastructure, procedures, equipment, and supplies (PIPES).MethodsA follow‐up assessment of 10 government hospitals in Sierra Leone was completed 42 months after an initial survey in 2008 using the PIPES tool. An index based on number of operating rooms, personnel, infrastructure, procedures, equipment, and supplies was calculated. An index was also calculated, using the 2008 data for comparison.ResultsMost hospitals demonstrated an increased index that correlated with site visits that verified improved conditions. Connaught Hospital in Sierra Leone had the highest score (9.2), consistent with its being the best equipped and staffed Ministry of Health and Sanitation facility. Makeni District Hospital had the greatest increase, from 3.8 to 7.5, consistent with a newly constructed facility.DiscussionThe PIPES tool was easily administered at hospitals in Sierra Leone and an index was found useful. Surgical capacity in Sierra Leone improved between 2008 and 2011, as demonstrated by an increase in the overall PIPES indices.
Effect of Mixed Nanobubble and Microbubble Liquids on the Washing Rate of Cloth in an Alternating Flow
Authors: Ushida Akiomi , Hasegawa Tomiichi , Takahashi Naoyuki , Nakajima Toshiyuki , Murao Shotaro , Narumi Takatsune , Uchiyama Hiroshige 
Published: April 2012

AbstractIt is well‐known that laundry waste water contributes to water pollution, and the need to reduce the amount of detergent used is widely recognized. Predominantly, research has focused on the washing effects of microbubbles and nanobubbles, and mechanical work was found to account for about 50 % of the washing effect on the cloth. In the present research, mixed nanobubble and microbubble water and four types of surfactants (including a commercial cleaning liquid) were investigated in an alternating flow system. The nanobubble water achieved a washing rate greater than that of ion‐exchanged water. However, the microbubble water had the same washing rate as ion‐exchanged water. Moreover, nanobubbles mixed with an aqueous solution of surfactant exhibited a washing rate that depended on the ionization of the surfactant: the mixture with nanobubbles and anionic surfactant exhibited a washing rate that was higher than that of aqueous anionic surfactant solution without nanobubbles. The surface tensions of nanobubble water and mixed nanobubble anionic surfactant were lower than those without nanobubble, respectively. Also, there was no advantage in mixed microbubble liquids. These results provide evidence of an enhanced washing effect by nanobubble mixtures in liquids.
Effect of polyvinylpyrrolidone on sperm function and early embryonic development following intracytoplasmic sperm injection in human assisted reproduction
Authors: Kato Yoku , Nagao Yoshikazu 
Published: April 2012

AbstractThe objective here was to review the effects of polyvinylpyrrolidone (PVP) upon sperm function and embryonic development in humans. PVP has been used successfully in intracytoplasmic sperm injection (ICSI) to facilitate the handling and immobilization of sperm for both domestic animals and humans. In our previous reports, PVP solution exists locally in embryos injected during the early developmental period, and also exerts influence over the developmental capacity of such embryos. In other reports, PVP causes significant damage to sperm membranes that can be detected by transmission electron microscopy, and has been associated with chromosomal abnormalities in pregnancy derived from ICSI embryos. In some Japanese clinics, PVP‐free media has been used for sperm immobilization in order to optimise safety. Consequently, it is strongly suggested that the success rate of fertilization and clinical pregnancy could be improved by using PVP‐free solution for human ICSI. In conclusion, our interpretation of the available data is to perform ICSI without PVP or select a lower concentration of PVP solution in order to reduce safety for pregnancy and children born via ICSI.
A 30 T pulsed magnet with conical bore for synchrotron powder diffraction
Authors: Billette J. , Duc F. , Frings P. , Nardone M. , Zitouni A. , Detlefs C. , Roth T. , Crichton W. , Lorenzo J. E. , Rikken G. L. J. A. 
Published: April 2012

We report on the design, construction, and operation of a horizontal field, 30 T magnet system with a conical bore optimized for synchrotron x-ray powder diffraction. The magnet offers ±31° optical access downstream of the sample, which allows to measure a sufficiently large number of Debye rings for an accurate crystal structure analysis. Combined with a 290 kJ generator, magnetic field pulses of 60 ms length were generated in the magnet, with a rise time of 4.1 ms and a repetition rate of 6 pulses/h at 30 T. The coil is mounted inside a liquid nitrogen bath. A liquid helium flow cryostat reaches into the coil and allows sample temperature between 5 and 250 K. The setup was used on the European Synchrotron Radiation Facility beamlines ID20 and ID06.
Timing of Yellow Perch Otolith Annulus Formation and Relationship between Fish and Otolith Lengths
Authors: Blackwell Brian G. , Kaufman Todd M. 
Published: April 2012

Abstract
We estimated the timing of annulus formation and the relationship between otolith radius length (whole view) and total length (TL) in yellow perch Perca flavescens from South Dakota lakes. Marginal increment analysis indicated that a single opaque band is formed during the summer months and that the timing of annulus formation varies with fish age. The lowest marginal increment measurements (i.e., those suggesting that annulus formation was recently completed) were most likely to occur in July, but at Waubay Lake the lowest increment for some cohorts was observed in August. Fish of age 4 or less were more likely to complete annulus formation during June. Personnel responsible for aging otoliths need to be aware of the differential timing of annulus formation. Significant relationships were observed between yellow perch TL and otolith radius length for 49 populations. Nearly all (98%) of the regression intercepts were negative. Back-calculated TLs were estimated from otolith annulus measurements using the direct proportion method and compared with the TLs previously measured for three populations. The back-calculated TL estimates were similar to the previously observed TLs, suggesting that the direct proportion method can be used to back-calculate TLs from yellow perch otoliths.
Received February 18, 2011; acceptdate November 30, 2011
Fast protein binding site comparisons using visual words representation
Authors: Pang Bin , Zhao Nan , Korkin Dmitry , Shyu Chi-Ren 
Published: April 2012

Abstract
Motivation: Finding geometrically similar protein binding sites is crucial for understanding protein functions and can provide valuable information for protein–protein docking and drug discovery. As the number of known protein–protein interaction structures has dramatically increased, a high-throughput and accurate protein binding site comparison method is essential. Traditional alignment-based methods can provide accurate correspondence between the binding sites but are computationally expensive.
Results: In this article, we present a novel method for the comparisons of protein binding sites using a ‘visual words’ representation (PBSword). We first extract geometric features of binding site surfaces and build a vocabulary of visual words by clustering a large set of feature descriptors. We then describe a binding site surface with a high-dimensional vector that encodes the frequency of visual words, enhanced by the spatial relationships among them. Finally, we measure the similarity of binding sites by utilizing metric space operations, which provide speedy comparisons between protein binding sites. Our experimental results show that PBSword achieves a comparable classification accuracy to an alignment-based method and improves accuracy of a feature-based method by 36% on a non-redundant dataset. PBSword also exhibits a significant efficiency improvement over an alignment-based method.
Availability: PBSword is available at http://proteindbs.rnet.missouri.edu/pbsword/pbsword.html
Contact: shyuc@missouri.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Detection of differentially expressed segments in tiling array data
Authors: Otto Christian , Reiche Kristin , Hackermüller Jörg 
Published: April 2012

AbstractMotivation: Tiling arrays have been a mainstay of unbiased genome-wide transcriptomics over the last decade. Currently available approaches to identify expressed or differentially expressed segments in tiling array data are limited in the recovery of the underlying gene structures and require several parameters that are intensity-related or partly dataset-specific.Results: We have developed TileShuffle, a statistical approach that identifies transcribed and differentially expressed segments as significant differences from the background distribution while considering sequence-specific affinity biases and cross-hybridization. It avoids dataset-specific parameters in order to provide better comparability of different tiling array datasets, based on different technologies or array designs. TileShuffle detects highly and differentially expressed segments in biological data with significantly lower false discovery rates under equal sensitivities than commonly used methods. Also, it is clearly superior in the recovery of exon–intron structures. It further provides window z-scores as a normalized and robust measure for visual inspection.Availability: The R package including documentation and examples is freely available at http://www.bioinf.uni-leipzig.de/Software/TileShuffle/Contact: joerg.hackermueller@ufz.deSupplementary information: Supplementary data are available at Bioinformatics online.
Approximate probabilistic analysis of biopathway dynamics
Authors: Liu Bing , Hagiescu Andrei , Palaniappan Sucheendra K. , Chattopadhyay Bipasa , Cui Zheng , Wong Weng-Fai , Thiagarajan P. S. 
Published: April 2012

Abstract
Motivation: Biopathways are often modeled as systems of ordinary differential equations (ODEs). Such systems will usually have many unknown parameters and hence will be difficult to calibrate. Since the data available for calibration will have limited precision, an approximate representation of the ODEs dynamics should suffice. One must, however, be able to efficiently construct such approximations for large models and perform model calibration and subsequent analysis.
Results: We present a graphical processing unit (GPU) based scheme by which a system of ODEs is approximated as a dynamic Bayesian network (DBN). We then construct a model checking procedure for DBNs based on a simple probabilistic linear time temporal logic. The GPU implementation considerably extends the reach of our previous PC-cluster-based implementation (Liu et al., 2011b). Further, the key components of our algorithm can serve as the GPU kernel for other Monte Carlo simulations-based analysis of biopathway dynamics. Similarly, our model checking framework is a generic one and can be applied in other systems biology settings.
We have tested our methods on three ODE models of bio-pathways: the epidermal growth factor–nerve growth factor pathway, the segmentation clock network and the MLC-phosphorylation pathway models. The GPU implementation shows significant gains in performance and scalability whereas the model checking framework turns out to be convenient and efficient for specifying and verifying interesting pathways properties.
Availability: The source code is freely available at http://www.comp.nus.edu.sg/~rpsysbio/pada-gpu/
Contact: thiagu@comp.nus.edu.sg
Supplementary information: Supplementary data are available at Bioinformatics online.
A comprehensive computational model of facilitated diffusion in prokaryotes
Authors: Zabet Nicolae Radu , Adryan Boris 
Published: April 2012

Abstract
Motivation: Gene activity is mediated by site-specific transcription factors (TFs). Their binding to defined regions in the genome determines the rate at which their target genes are transcribed.
Results: We present a comprehensive computational model of the search process of TF for their genomic target site(s). The computational model considers: the DNA sequence, various TF species and the interaction of the individual molecules with the DNA or between themselves. We also demonstrate a systematic approach how to parametrize the system using available experimental data.
Contact: n.r.zabet@gen.cam.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Oocyte development and maturity classification of boarfish (Capros aper) in the Northeast Atlantic
Authors: Farrell Edward D. , Hüssy Karin , Coad Julie O. , Clausen Lotte W. , Clarke Maurice W. 
Published: April 2012

AbstractFarrell, E. D., Hüssy, K., Coad, J. O., Clausen, L. W., and Clarke, M. W. 2012. Oocyte development and maturity classification of boarfish (Capros aper) in the Northeast Atlantic. – ICES Journal of Marine Science, 69: 498–507. This study presents the first detailed investigation of the oocyte development and maturity classification of boarfish, Capros aper, which has recently become the target of an industrial fishery in the Northeast Atlantic. A total of 2014 boarfish were collected from January to December 2010. Mature male and female boarfish were sexually dimorphic and could be readily identified based on external characteristics. A comprehensive maturity scale was developed, which indicated that the length at 50% maturity for males and females was 9.7 cm total length. Female boarfish were observed to spawn in Irish waters in June and July. Once spawning ceased the remaining mature oocytes were resorbed. Preliminary analysis of reproductive strategy indicates that the boarfish is likely an asynchronous batch spawner with indeterminate fecundity.
Assessing fishery footprints and the trade-offs between landings value, habitat sensitivity, and fishing impacts to inform marine spatial planning and an ecosystem approach
Authors: Jennings S. , Lee J. , Hiddink J. G. 
Published: April 2012

Abstract
Jennings, S., Lee, J., and Hiddink, J. G. 2012. Assessing fishery footprints and the trade-offs between landings value, habitat sensitivity, and fishing impacts to inform marine spatial planning and an ecosystem approach. – ICES Journal of Marine Science, 69: 1053–1063. European and national policy commitments require further integration of fisheries and environmental management. We measured fishery footprints and assessed trade-offs between landings value, habitat sensitivity, and beam trawling impacts in UK territorial waters in the southern and central North Sea where marine spatial planning is underway and a network of Marine Protected Areas has been proposed. For fleets (UK and non-UK) and years (2006–2010) considered, total trawled area included extensive ‘margins’ that always accounted for a smaller proportion of total fishing effort and value (proportions investigated were ≤10, 20, or 30%) than their proportional contribution to total habitat sensitivity and trawling impact. Interannual and fleet-related differences in the distribution and intensity of trawling activity, driven by location choice and fisheries regulations, had more influence on overall trawling impacts than the exclusion of beam trawlers from a proposed network of Marine Protected Areas. If reducing habitat impacts is adopted as an objective of fisheries or environmental management, then the direct management of fishing footprints, e.g. by defining fishing grounds that exclude existing margins, can disproportionately reduce trawling impacts per unit effort or value.
Documentation of an Extended Latent Infection Period by Phakopsora pachyrhizi, the Soybean Rust Pathogen
Authors: Ward N. A. , Schneider R. W. , Robertson C. L. 
Published: April 2012

Phakopsora pachyrhizi, the soybean rust pathogen, overwinters on kudzu in the southern United States. However, even with severely affected kudzu adjacent to soybean fields, disease symptoms do not occur on soybeans until plants are in mid-reproductive stages of growth during mid to late summer. These observations suggested that soybeans are exposed to airborne inoculum of the pathogen long before symptoms occur, and we hypothesized that these plants may be latently infected. This hypothesis was confirmed by using quantitative real-time PCR (qPCR) to detect the rust pathogen in soybean leaves 18 to 60 days before symptoms were observed. Additionally, DNA of P. pachyrhizi increased only slightly until one week before symptoms developed. Results from this study documented that soybeans can become infected by the rust pathogen during early stages of plant growth, but symptoms often develop during the mid-reproductive stages. This extended latent infection period may be an optimum time for fungicide applications. Accepted for publication 12 December 2011. Published 21 March 2012.
Evaluation of Soybean Genotypes for Resistance to Three Seed-borne Diseases
Authors: Mengistu Alemu , Arelli P. A. , Bellaloui Nacer , Bond J. P. , Shannon G. J. , Wrather A. J. , Rupe J. C. , Chen P. , Little C. R. , Canaday C. H. , Newman M. A. , Pantalone V. R. 
Published: April 2012

Seed-borne diseases of soybeans caused by Phomopsis longicolla (Phomopsis seed decay), Cercospora kukuchii (purple seed stain), and M. phaseolina (charcoal rot) are economically important diseases that affect seed quality. Commercial cultivars marketed as resistant to all three diseases are not available. Reactions of 27 maturity group (MG) III, 30 early MG IV, 33 late MG IV, and 53 MG V genotypes were evaluated for resistance to these pathogens during the 2006 to 2008 growing season in the same field that had been in no-till production, not irrigated, and naturally and artificially infested. There was great variation in seed infection among genotypes and years, indicating the value of screening genotypes over multiple years. Some genotypes were resistant to these pathogens in one, two, or in all three years. Genotypes, DP 3478 (early MG IV), and RO1-769F (MG V) were resistant and DG4460 was moderately resistant to P. longicolla infection across three years. Genotypes AG3705 and FFR3990 (MG III) and DC20300, DC7816, Stoddard, and Ozark (MG V), were resistant to C. kukuchii infection during all three years. Ten genotypes in MG III, eight in early MG IV, seven in late MG IV, and 14 in MG V had no seed infection by M. phaseolina in all three years. These results indicate that seed infection comparison to these pathogens among genotypes should be made over several years, or false conclusions about resistance to any of the three pathogens may be made when disease is assessed for limited period of time. The genotypes identified as having resistance to each or combinations of the seed-borne diseases across the three years could be useful as a source for resistance in improving soybean seed quality. Accepted for publication 20 December 2012. Published 21 March 2012.
Higher-order awareness, misrepresentation and function
Authors: Rosenthal David 
Published: April 2012

Conscious mental states are states we are in some way aware of. I compare higher-order theories of consciousness, which explain consciousness by appeal to such higher-order awareness (HOA), and first-order theories, which do not, and I argue that higher-order theories have substantial explanatory advantages. The higher-order nature of our awareness of our conscious states suggests an analogy with the metacognition that figures in the regulation of psychological processes and behaviour. I argue that, although both consciousness and metacognition involve higher-order psychological states, they have little more in common. One thing they do share is the possibility of misrepresentation; just as metacognitive processing can misrepresent one's cognitive states and abilities, so the HOA in virtue of which one's mental states are conscious can, and sometimes does, misdescribe those states. A striking difference between the two, however, has to do with utility for psychological processing. Metacognition has considerable benefit for psychological processing; in contrast, it is unlikely that there is much, if any, utility to mental states' being conscious over and above the utility those states have when they are not conscious.
Self‐reported nutritional knowledge and the acceptance of health‐related food benefit claims
Authors: Baglione Stephen L. , Tucci Louis A. , Stanton John L. 
Published: April 2012

PurposeThe purpose of this study is to determine whether reported nutritional knowledge and the acceptance of benefit claims for a fresh produce item is related to changes in preference in order to provide food marketers insight and guidance into giving consumers more information to change beliefs and preferences, using health‐benefit claims to position their brands as offering ingredients, e.g. Lycopene which may prevent serious illnesses such as heart disease and cancer.Design/methodology/approachThe sample was drawn from an internet panel maintained by Markettools, Inc, a respected market research company in the USA. A total of 594 respondents were surveyed. Besides demographic questions, respondents were asked about their knowledge of nine nutrients. Basic nutrient knowledge was estimated through a one‐sample t‐test tested against a value of two on a 1‐4 scale. Respondents evaluated eight benefit statements regarding the health benefits of mushrooms. After reading each statement, respondents indicated their likelihood of purchasing fresh mushrooms and were asked about the believability, favorability, and uniqueness of each statement.FindingsThe results indicate that health‐related food benefit claims are better accepted by female respondents who claim to be nutritionally knowledgeable and who are older. Three hypotheses related to nutritional knowledge and beliefs showed that knowledge and beliefs have an effect but the effect varied by nutrient and nutrient cluster. In particular, knowledge of esoteric nutrients such as Pantothenic Acid was associated with acceptance of health‐related claims.Practical implicationsFood marketers are spending millions of dollars/pounds/euros on informing people of the nutrient content and health benefits of their foods. However, this money can be better spent if one first understands the existing levels of nutritional knowledge and the specific nutrients that motivate change in preference or buying intention.Originality/valueThis paper builds on the existing body of knowledge using additional statistical techniques to cluster nutrients and to provide a demonstration on a fresh produce food group not currently investigated in the literature. It suggests that food marketers need to gather more information on their consumers to target their health and nutrition message to the proper (more receptive) audience.