bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhancing genome assemblies by integrating non-sequence based data
Authors: Heider Thomas N , Lindsay James , Wang Chenwei , O’Neill Rachel J , Pask Andrew J 
Published: April 2011

Abstract

Introduction
Many genome projects were underway before the advent of high-throughput sequencing and have thus been supported by a wealth of genome information from other technologies. Such information frequently takes the form of linkage and physical maps, both of which can provide a substantial amount of data useful in de novo sequencing projects. Furthermore, the recent abundance of genome resources enables the use of conserved synteny maps identified in related species to further enhance genome assemblies.

Methods
The tammar wallaby (Macropus eugenii) is a model marsupial mammal with a low coverage genome. However, we have access to extensive comparative maps containing over 14,000 markers constructed through the physical mapping of conserved loci, chromosome painting and comprehensive linkage maps. Using a custom Bioperl pipeline, information from the maps was aligned to assembled tammar wallaby contigs using BLAT. This data was used to construct pseudo paired-end libraries with intervals ranging from 5-10 MB. We then used Bambus (a program designed to scaffold eukaryotic genomes by ordering and orienting contigs through the use of paired-end data) to scaffold our libraries. To determine how map data compares to sequence based approaches to enhance assemblies, we repeated the experiment using a 0.5× coverage of unique reads from 4 KB and 8 KB Illumina paired-end libraries. Finally, we combined both the sequence and non-sequence-based data to determine how a combined approach could further enhance the quality of the low coverage de novo reconstruction of the tammar wallaby genome.

Results
Using the map data alone, we were able order 2.2% of the initial contigs into scaffolds, and increase the N50 scaffold size to 39 KB (36 KB in the original assembly). Using only the 0.5× paired-end sequence based data, 53% of the initial contigs were assigned to scaffolds. Combining both data sets resulted in a further 2% increase in the number of initial contigs integrated into a scaffold (55% total) but a 35% increase in N50 scaffold size over the use of sequence-based data alone.

Conclusions
We provide a relatively simple pipeline utilizing existing bioinformatics tools to integrate map data into a genome assembly which is available at http://www.mcb.uconn.edu/fac.php?name=paska. While the map data only contributed minimally to assigning the initial contigs to scaffolds in the new assembly, it greatly increased the N50 size. This process added structure to our low coverage assembly, greatly increasing its utility in further analyses.
Deciphering transcription factor binding patterns from genome-wide high density ChIP-chip tiling array data
Authors: Li Juntao , Zhu Lei , Eshaghi Majid , Liu Jianhua , Karuturi Krishna Murthy R 
Published: April 2011

Abstract

Background
The binding events of DNA-interacting proteins and their patterns can be extensively characterized by high density ChIP-chip tiling array data. The characteristics of the binding events could be different for different transcription factors. They may even vary for a given transcription factor among different interaction loci. The knowledge of binding sites and binding occupancy patterns are all very useful to understand the DNA-protein interaction and its role in the transcriptional regulation of genes.

Results
In the view of the complexity of the DNA-protein interaction and the opportunity offered by high density tiled ChIP-chip data, we present a statistical procedure which focuses on identifying the interaction signal regions instead of signal peaks using moving window binomial testing method and deconvolving the patterns of interaction using peakedness and skewness scores. We analyzed ChIP-chip data of 4 different DNA interacting proteins including transcription factors and RNA polymerase in fission yeast using our procedure. Our analysis revealed the variation of binding patterns within and across different DNA interacting proteins. We present their utility in understanding transcriptional regulation from ChIP-chip data.

Conclusions
Our method can successfully detect the signal regions and characterize the binding patterns in ChIP-chip data which help appropriate analysis of the ChIP-chip data.
Novel Method for Generating Large Mesopores in an Amorphous Silica–Alumina by Controlling the Pore Size with the Gel Skeletal Reinforcement and Its Catalytic Cracking Properties as a Catalyst Matrix
Authors: Ishihara Atsushi , Nakajima Kohei , Hirado Motoki , Hashimoto Tadanori , Nasu Hiroyuki 
Published: April 2011

Abstract
The pore size of amorphous silica and silica–alumina with large mesopores was controlled for the first time in the range of 5 to 30 nm by gel skeletal reinforcement. The conversion and the ratio of multi-branched to single-branched products increased with increasing the pore diameter of silica–alumina in catalytic cracking of n-dodecane with its use as a matrix.
Oxygen Permeability Change of Polyphenylacetylene Derivatives by Postfunctional TCNE Addition
Authors: Li Yongrong , Hyakutake Tsuyoshi , Michinobu Tsuyoshi 
Published: April 2011

Abstract
Polyphenylacetylene derivatives substituted by dialkylanilino-appended alkyne side chains were synthesized by Rh-catalyzed polymerization. Improved oxygen barrier ability was achieved by the postfunctional, controlled introduction of four nitrile groups into the repeat unit of the polyphenylacetylene derivatives.
Estimation of organ-absorbed radiation doses during 64-detector CT coronary angiography using different acquisition techniques and heart rates: a phantom study
Authors: Matsubara Kosuke , Koshida Kichiro , Noto Kimiya , Takata Tadanori , Shimono Tetsunori , Kawashima Hiroko , Yamamoto Tomoyuki , Matsui Osamu 
Published: April 2011

Background Though appropriate image acquisition parameters allow an effective dose below 1 mSv for CT coronary angiography (CTCA) performed with the latest dual-source CT scanners, a single-source 64-detector CT procedure results in a significant radiation dose due to its technical limitations. Therefore, estimating the radiation doses absorbed by an organ during 64-detector CTCA is important. Purpose To estimate the radiation doses absorbed by organs located in the chest region during 64-detector CTCA using different acquisition techniques and heart rates. Material and Methods Absorbed doses for breast, heart, lung, red bone marrow, thymus, and skin were evaluated using an anthropomorphic phantom and radiophotoluminescence glass dosimeters (RPLDs). Electrocardiogram (ECG)-gated helical and ECG-triggered non-helical acquisitions were performed by applying a simulated heart rate of 60 beats per minute (bpm) and ECG-gated helical acquisitions using ECG modulation (ECGM) of the tube current were performed by applying simulated heart rates of 40, 60, and 90 bpm after placing RPLDs on the anatomic location of each organ. The absorbed dose for each organ was calculated by multiplying the calibrated mean dose values of RPLDs with the mass energy coefficient ratio. Results For all acquisitions, the highest absorbed dose was observed for the heart. When the helical and non-helical acquisitions were performed by applying a simulated heart rate of 60 bpm, the absorbed doses for heart were 215.5, 202.2, and 66.8 mGy for helical, helical with ECGM, and non-helical acquisitions, respectively. When the helical acquisitions using ECGM were performed by applying simulated heart rates of 40, 60, and 90 bpm, the absorbed doses for heart were 178.6, 139.1, and 159.3 mGy, respectively. Conclusion ECG-triggered non-helical acquisition is recommended to reduce the radiation dose. Also, controlling the patients’ heart rate appropriately during ECG-gated helical acquisition with ECGM is crucial.
Percutaneous radiofrequency ablation of renal cell carcinomas in patients with von Hippel Lindau disease previously undergoing a radical nephrectomy or repeated nephron-sparing surgery
Authors: Park Sung Yoon , Park Byung Kwan , Kim Chan Kyo , Lee Hyun Moo , Jeon Seong Soo , Seo Seong Il , Jeong Byong Chang , Choi Han Yong 
Published: April 2011

Background Radiofrequency ablation (RFA) is accepted as a minimally invasive treatment of renal cell carcinoma (RCC). However, RFA is not fully evaluated for treating RCC in patients with von Hippel Lindau (VHL) disease who cannot undergo surgery due to serious postoperative morbidity or mortality. Purpose To evaluate the role of RFA of RCC in patients with VHL disease previously undergoing renal surgery. Material and Methods Percutaneous RFA was performed for treating 14 RCCs in six patients who had undergone radical nephrectomy ( n = 3) or repeated nephron-sparing surgery ( n = 3). Treatment feasibility, complications, outcome, and the change of renal function were evaluated. Results To completely ablate 14 RCCs, 23 ablations during 12 sessions were necessary. Of 14 RCCs, nine were in proximity (<5 mm) to one or more following organs: bowel ( n = 4), ureteropelvic junction or pelvis ( n = 2), psoas muscle ( n = 2), vascular pedicle ( n = 1), and pancreas ( n = 1). Of 12 sessions, one major complication (pneumothorax) developed in one session (8%). No residual or recurrent tumors were identified at the ablation areas. However, new three solid tumors less than 1 cm in diameter developed during the follow-up period but ablation was withheld until these tumors had grown to more than 1 cm in size. The mean level of serum creatinine increased with 6.4% and the mean estimated glomerular filtration rate decreased by 12.8% after the last ablation compared to those before the initial ablation ( P < 0.05). Conclusion Despite technical difficulties, percutaneous RFA is a promising treatment for VHL patients who cannot undergo surgery because of excellent treatment outcome and minimal change of renal function.
Influence of adenosine on ventricular function measurements as part of a comprehensive stress perfusion magnetic resonance imaging study
Authors: Sievers Burkhard , Jacobi Liane , Sommer Philipp , Speiser Uwe , Schoen Steffen , Strasser Ruth H 
Published: April 2011

Background Stress-rest perfusion magnetic resonance imaging (MRI) has become one of the major indications for cardiovascular MRI. Standard multibreath hold short-axis image acquisition is the gold standard for LV function assessment and part of a comprehensive stress-rest perfusion MRI study, but takes up to 10 min. The total scan time could significantly be shortened when cine imaging would be performed between stress and rest perfusion. Purpose To systematically study whether adenosine, albeit its short half-life time, influences LV function measurements in this setting. Material and Methods Thirty-nine patients with suspected and/or known coronary artery disease underwent 3-Tesla adenosine (140 µg/min/kg) stress-rest perfusion MRI. A stack of short-axis slices covering the entire ventricles was acquired before and ≥3 min after adenosine infusion using standard multibreath-hold 2D steady-state free precession imaging. LV volumes (EDV, ESV), EF, and mass were calculated by the slice summation method, and wall motion was assessed using a 4-point scoring scale. Reproducibility was assessed by Bland-Altman statistics. Results EDV, ESV, EF, and mass were not significantly different between the two imaging time points (before versus after adenosine administration) in all patients ( P ≥ 0.346) and patients with impaired LV function ( P ≥ 0.718). Wall motion scores did not differ either ( P ≥ 0.124). Inter-observer variability before ( P ≥ 0.468) and after ( P ≥ 0.451) adenosine infusion was low. Conclusion Short-axis cine imaging for LV function assessment can accurately be performed between stress and rest imaging. These data demonstrate that potential effects of adenosine on LV function are of short duration, and propose a new time-saving imaging protocol without compromising accuracy.
Radiologic characteristics of sinonasal fungus ball: an analysis of 119 cases
Authors: Seo Young-Joon , Kim Jinna , Kim Kyubo , Lee Jeung-Gweon , Kim Chang-Hoon , Yoon Joo-Heon 
Published: April 2011

Background It is important to differentiate sinonasal fungus ball from non-fungal sinusitis and other forms of fungal sinusitis in order to determine the optimal treatment. In particular, a sinonasal fungus ball, a non-invasive fungal sinusitis, can be characterized by radiologic findings before surgery. Purpose To differentiate a sinonasal fungus ball from other types of sinusitis and determine optimal treatment on the basis of radiologic findings before surgery. Material and Methods We studied 119 patients with clinically and pathologically proven sinonasal fungus balls. Their condition was evaluated radiologically with contrast-enhanced CT (99 patients), non-contrast CT (18 patients) and/or MRI (17 patients) prior to sinonasal surgery. Results Calcifications were found in 78 of 116 (67.2%) patients who underwent CT scans for fungus ball. As opposed to non-contrast CT scans, contrast CT scans revealed hyperattenuating fungal ball in 82.8% and enhanced inflamed mucosa in 65.5% of the patients, respectively. On MRI, most sinonasal fungal balls showed iso- or hypointensity on T1-weighted images and marked hypointensity on T2-weighted images. Inflamed mucosal membranes were noted and appeared as hypointense on T1-weighted images (64.7%) and hyperintense on T2-weighted images (88.2%). Conclusion When there are no calcifications visible on the CT scan, a hyperattenuating fungal ball located in the central area of the sinus with mucosal thickening on enhanced CT scans is an important feature of a non-invasive sinonasal fungus ball. On MRI, a sinonasal fungus ball has typical features of a marked hypointense fungus ball with a hyperintense mucosal membrane in T2-weighted images. A contrast-enhanced CT scan or MRI provides sufficient information for the preoperative differentiation of a sinonasal fungus ball from other forms of sinusitis.
Dependence of Water Vapour Adsorption on the Polarity of the Graphene Surfaces of Multi-Wall Carbon Nanotubes
Authors: Bradley Robert H. , Andreu Aurik , Cassity Kelby , Osbeck Susan , Andrews Rodney , Meier Mark , Johnston Colin 
Published: April 2011

The adsorption of water by the graphene surfaces of multi-wall carbon nanotubes (MWCNTs) in either the untreated (4.3 atom% oxygen) or oxidised (22.3 atom% oxygen) surface states has been studied. Different concentrations of surface oxygen groups, which have been directly measured using XPS, give rise to distinctly different shapes of water adsorption isotherms. Those from the untreated materials follow the pressure axis which lends them a Type III character in the BDDT classification. However, since they display a clear point of inflection at the lowest pressure, they are strictly speaking Type II isotherms but indicative of relatively few polar interactions and weak water adsorptivity. In sharp contrast, the isotherms from the oxidised MWCNTs are typically Type II and are characterised by a marked positive curvature in their low pressure region due to the increased numbers of specific interactions occurring between water molecules and the polar surface oxygen groups. The water adsorption data were modelled by the equation of D'Arcy and Watt with a direct correlation being observed between the surface polarity parameters (amL and a0) and also as (the limiting water uptake) and the surface oxygen levels of the MWCNTs. The difference in polar surface energy was confirmed by measurements of the calorimetric enthalpies of immersion in water (Δhi), which were −54 mJ/m2 for the untreated and −192 mJ/m2 for the oxidised materials. These values also reflect the difference in the integral net enthalpies of adsorption for the two hydrophilic surfaces: a value of ca. −35 mJ/m2 being obtained for an oxygen-free (hydrophobic) surface. Water adsorption on these hydrophilic graphene surfaces was shown to occur by specific hydrogen bonding and was therefore strongly dependent on the numbers of oxygen-containing polar surface sites. This behaviour is well known for other types of porous and non-porous carbon materials and is also predicted for carbon nanotubes by molecular simulation studies. The work described herein therefore provides early experimental confirmation of the quantitative role of surface oxygen chemistry in determining the water adsorption character of MWCNT graphene surfaces; it also validates previous simulation studies.
Adsorption of Bovine Serum Albumin onto Mesocellular Silica Foams with Differently Sized Cells and Windows
Authors: Sezões F. , Carrott M.M.L. Ribeiro , Mourão P.A.M. , Carrott P.J.M. 
Published: April 2011

As a model protein with quite large dimensions, Bovine Serum Albumin (BSA) has been used to evaluate the influence of the distinct pore structural characteristics of three mesocellular foam (MCF) materials prepared with or without the addition of ammonium fluoride and with varying 1,3,5-trimethylbenzene/Pluronic P123 (TMB/P123) ratios. SBA-15 was also studied for comparative purposes. Characterisation by X-ray diffraction and electron microscopy confirmed the characteristic spheroid cell structure of the MCF pores. Nitrogen adsorption/desorption isotherms at 77 K revealed the different pore structural parameters of the MCF, viz. pore volume (1.8–2.4 cm3/g), cell size (24.6–28.5 nm) and window size (11.3–17.3 nm), as obtained by the NLDFT method. The equilibrium adsorption isotherms and the kinetic adsorption data for BSA at 298 K and pH 5 were well fitted by the Langmuir model and pseudo-second-order kinetic model, respectively. The results showed that adsorption onto the material possessing a window size of 11.3 nm was mostly restricted to the external surface, while a considerable increase in the maximum adsorption capacity from 120 mg/g to 500–600 mg/g was observed when the window size was above the critical dimension of 13.9 nm. In the latter cases, the maximum adsorption capacities could be related to the pore volume rather than to the total surface area. The confined BSA molecules were strongly immobilised in the cells, since only a small proportion was desorbed from the material with windows of 17.3 nm dimensions on contact with a buffer solution of pH 7.
Effect of Façade Shape for the Acoustic Protection of Buildings
Authors: Busa Lucia , Secchi Simone , Baldini Stefano 
Published: April 2011

Façade sound insulation can be improved by using high performance components or by modifying the shape of the façade. In many cases, when high acoustic insulation levels are required, the use of high performance components cannot be sufficient, for technical or economic reasons. The European standard EN 12354-3 [1] gives a simplified method to estimate the influence of the façade shape in the reduction of sound pressure level at the outside of the building envelope. In particular, the influence of the façade is evaluated for a number of building typologies as a function of the general direction of the incoming sound and of the acoustic absorption coefficient of the surface of the underside of the balcony. In the paper, the results of a study on the influence of the façade shape on the incoming sound are evaluated with reference to a great number of different typologies of buildings facades. The study has been carried out by means of a prediction software based on the modified theory of the ray tracing (pyramid tracing). Moreover, some of the configurations analyzed with the prediction software have been tested also in a scale model. With reference to a typical urban configuration, results are expressed as level difference between the simple plane façade and the façade with different kind of shielding.
CUDA Memory Optimizations for Large Data-Structures in the Gravit Simulator
Authors: Siegel Jakob , Ributzka Juergen , Li Xiaoming 
Published: April 2011

Modern GPUs open a completely new field to optimize embarrassingly parallel algorithms. Implementing an algorithm on a GPU confronts the programmer with a new set of challenges for program optimization. Especially tuning the program for the GPU memory hierarchy whose organization and performance implications are radically different from those of general purpose CPUs; and optimizing programs at the instruction-level for the GPU. In this paper we analyze different approaches for optimizing the memory usage and access patterns for GPUs and propose a class of memory layout optimizations that can take full advantage of the unique memory hierarchy of NVIDIA CUDA. Furthermore, we analyze some classical optimization techniques and how they effect the performance on a GPU. We used the Gravit gravity simulator to demonstrate these optimizations. The final optimized GPU version achieves a 87× speedup compared to the original CPU version. Almost 30% of this speedup are direct results of the optimizations discussed in this paper.
Characterization of the Effects of Droplet Size, Air Blast Strength, and Angle on Spray Distribution and Efficacy of a Buffalo Turbine Barrier Treatment Sprayer
Authors: Bonds Jane A. S. , Mulla Cindy , Hunter Ed 
Published: April 2011

Abstract
A Buffalo Turbine barrier treatment sprayer was characterized physically and biologically over a range of application settings. The effects of three increasing droplet size distributions, two air blast strengths, and three blower arm angles (65°, 80°, and 90°) were measured via water sensitive papers and residual contact bioassay. The data from the water sensitive papers provided information on how machine setting influenced the deposition through the canopy. For the canopy under investigation, directing the spray straight into the canopy (90° blower angle) led to the highest deposit volumes. As droplet size distributions increased no significant change in the volume deposited was observed. The increase in air blast strength from low to high had no overall effect on the volume deposited, but the low air blast strength did show a successive loss in volume with distance into the canopy. Whereas the high air blast strength only showed a loss in volume at the furthest distance from the sprayer. Mosquito mortality did not correlate with volume deposited. Mosquito mortality was greatest with the intermediate blower arm angle (80°). The only parameter that correlated with mortality was uniformity of deposits over surfaces. It is suggested from both quantitative and qualitative observations that uniformity was the primary deposition parameter affecting control. The methods set forth in this study are simple and inexpensive our aim is to introduce them a standard methods for optimizing barrier treatment applications for vegetative barrier treatments.
Shear and Axial Load Measurement Device for Anchors in Concrete
Authors: Hoehler Matthew S. , Dowell Robert K. , Watkins Derrick A. 
Published: April 2011

Abstract
This paper describes the construction, calibration and experimental validation of a test apparatus to measure axial and shear forces in anchors. Accurate measurement of anchor shear force has historically proven technically challenging. The measurement device, which was developed to capture anchor load distributions on nonstructural components anchored to concrete by multiple post-installed anchors during earthquake loading, makes possible the study of previously inaccessible anchorage behavior. The device described in this paper was designed for single anchors, however, the concept can be extended to larger groups of anchors and may have application in other areas of research and testing.