bluuebunny/crossref_metadata_2025_split huggingface dataset:
Semantically linking and browsing PubMed abstracts with gene ontology
Authors: Vanteru Bhanu C , Shaik Jahangheer S , Yeasin Mohammed 
Published: March 2008

AbstractBackgroundThe technological advances in the past decade have lead to massive progress in the field of biotechnology. The documentation of the progress made exists in the form of research articles. The PubMed is the current most used repository for bio-literature. PubMed consists of about 17 million abstracts as of 2007 that require methods to efficiently retrieve and browse large volume of relevant information. The State-of-the-art technologies such as GOPubmed use simple keyword-based techniques for retrieving abstracts from the PubMed and linking them to the Gene Ontology (GO). This paper changes the paradigm by introducing semantics enabled technique to link the PubMed to the Gene Ontology, called, SEGOPubmed for ontology-based browsing. Latent Semantic Analysis (LSA) framework is used to semantically interface PubMed abstracts to the Gene Ontology.ResultsThe Empirical analysis is performed to compare the performance of the SEGOPubmed with the GOPubmed. The analysis is initially performed using a few well-referenced query words. Further, statistical analysis is performed using GO curated dataset as ground truth. The analysis suggests that the SEGOPubmed performs better than the classic GOPubmed as it incorporates semantics.ConclusionsThe LSA technique is applied on the PubMed abstracts obtained based on the user query and the semantic similarity between the query and the abstracts. The analyses using well-referenced keywords show that the proposed semantic-sensitive technique outperformed the string comparison based techniques in associating the relevant abstracts to the GO terms. The SEGOPubmed also extracted the abstracts in which the keywords do not appear in isolation (i.e. they appear in combination with other terms) that could not be retrieved by simple term matching techniques.
An integrative approach to characterize disease-specific pathways and their coordination: a case study in cancer
Authors: Xu Min , Kao Ming-Chih J , Nunez-Iglesias Juan , Nevins Joseph R , West Mike , Zhou Xianghong Jasmine 
Published: March 2008

Abstract

Background
The most common application of microarray technology in disease research is to identify genes differentially expressed in disease versus normal tissues. However, it is known that, in complex diseases, phenotypes are determined not only by genes, but also by the underlying structure of genetic networks. Often, it is the interaction of many genes that causes phenotypic variations.

Results
In this work, using cancer as an example, we develop graph-based methods to integrate multiple microarray datasets to discover disease-related co-expression network modules. We propose an unsupervised method that take into account both co-expression dynamics and network topological information to simultaneously infer network modules and phenotype conditions in which they are activated or de-activated. Using our method, we have discovered network modules specific to cancer or subtypes of cancers. Many of these modules are consistent with or supported by their functional annotations or their previously known involvement in cancer. In particular, we identified a module that is predominately activated in breast cancer and is involved in tumor suppression. While individual components of this module have been suggested to be associated with tumor suppression, their coordinated function has never been elucidated. Here by adopting a network perspective, we have identified their interrelationships and, particularly, a hub gene PDGFRL that may play an important role in this tumor suppressor network.

Conclusion
Using a network-based approach, our method provides new insights into the complex cellular mechanisms that characterize cancer and cancer subtypes. By incorporating co-expression dynamics information, our approach can not only extract more functionally homogeneous modules than those based solely on network topology, but also reveal pathway coordination beyond co-expression.
Functional diversity of HIV-1 envelope proteins expressed by contemporaneous plasma viruses
Authors: Nora Tamara , Bouchonnet Francine , Labrosse Béatrice , Charpentier Charlotte , Mammano Fabrizio , Clavel François , Hance Allan J 
Published: March 2008

AbstractBackgroundNumerous studies have shown that viral quasi-species with genetically diverse envelope proteins (Env) replicate simultaneously in patients infected with the human immunodeficiency virus type 1 (HIV-1). Less information is available concerning the extent that envelope sequence diversity translates into a diversity of phenotypic properties, including infectivity and resistance to entry inhibitors.MethodsTo study these questions, we isolated genetically distinct contemporaneous clonal viral populations from the plasma of 5 HIV-1 infected individuals (n = 70), and evaluated the infectivity of recombinant viruses expressing Env proteins from the clonal viruses in several target cells. The sensitivity to entry inhibitors (enfuvirtide, TAK-799), soluble CD4 and monoclonal antibodies (2G12, 48d, 2F5) was also evaluated for a subset of the recombinant viruses (n = 20).ResultsEven when comparisons were restricted to viruses with similar tropism, the infectivity for a given target cell of viruses carrying different Env proteins from the same patient varied over an approximately 10-fold range, and differences in their relative ability to infect different target cells were also observed. Variable region haplotypes associated with high and low infectivity could be identified for one patient. In addition, clones carrying unique mutations in V3 often displayed low infectivity. No correlation was observed between viral infectivity and sensitivity to inhibition by any of the six entry inhibitors evaluated, indicating that these properties can be dissociated. Significant inter-patient differences, independent of infectivity, were observed for the sensitivity of Env proteins to several entry inhibitors and their ability to infect different target cells.ConclusionThese findings demonstrate the marked functional heterogeneity of HIV-1 Env proteins expressed by contemporaneous circulating viruses, and underscore the advantage of clonal analyses in characterizing the spectrum of functional properties of the genetically diverse viral populations present in a given patient.
Rapid HPLC Measurement of Thiamine and Its Phosphate Esters in Whole Blood
Authors: Lu Jun , Frank Elizabeth L 
Published: March 2008

Abstract
Background: Thiamine (vitamin B1) deficiency is associated with severe diseases such as beriberi and Wernicke encephalopathy. Although most Americans have sufficient dietary intake, thiamine deficiency is observed in the alcohol-dependent and elderly populations. Measurement of thiamine concentration in whole blood provides an assessment of vitamin B1 status in at-risk individuals.
Method: We used TCA to precipitate proteins in whole blood. Thiamine and its phosphate esters were derivatized using potassium ferricyanide to thiochromes, which were separated by gradient elution on a reversed-phase HPLC column and detected by fluorescence. The method was validated for linearity, limit of quantification, imprecision, accuracy, and interference. Results obtained with this method were compared with those produced by the method currently used in our clinical laboratory. Reference values of thiamine and its phosphate esters were determined in samples obtained from self-reported healthy adults who were not taking vitamin supplements. To shorten analysis time, our method used whole blood rather than washed erythrocytes, did not require lengthy enzymatic dephosphorylation, and had a simple mobile phase.
Results: The method was linear to 4000 nmol/L. The lower limit of quantification was 3 nmol/L. The within-run CV was &lt;3.5% and total CV was &lt;9.4%. This method correlated with our current method (r = 0.97). Approximately 90% of the total thiamine content in whole blood was present as thiamine diphosphate (TDP). The means (ranges) for an apparently healthy population were 114 (70–179) nmol/L for TDP and 125 (75–194) nmol/L for total thiamine. Results for separation and measurement of free thiamine and thiamine phosphate esters in whole blood were obtained within 5.5 min.
Conclusion: We developed an HPLC method that allows separation and measurement of free thiamine and thiamine phosphate esters in whole blood and provides more rapid results than other methods.
Direct Shear Testing of a Marginal Material Using a Large Shear Box
Authors: Nakao Tomoyo , Fityus Stephen 
Published: March 2008

Abstract
In Australia, Q181C Test Method of Direct Shear Testing to estimate the Effective Angle of Internal Friction at Constant Volume Conditions for Granular (Coarse Grained) Materials is commonly applied to assess the suitability of backfills for reinforced earth walls. This paper presents a comparison between the results of three series of shear box tests on a typical ripped rock material, of marginal quality, that might be considered as a possible backfill material for a reinforced earth wall. Tests performed used 300 mm and 60 mm shear boxes, soil samples prepared to sub-19 mm and sub-4.75 mm sizes, and a range of shearing rates. The effect of pre-testing samples was also considered. The results show that accurate effective friction parameter measurements for coarse grained, granular backfill soils require the use of fresh soil specimens for each shearing test; the use of a large shear box that can accommodate soils with relatively large particles; and careful selection of shearing rates so that shearing takes place under drained conditions. If the above requirements are compromised, the measured effective friction angle is likely to be a significant under-estimate of the true effective friction angle, increasing the likelihood of the material failing to meet prescribed material quality standards.
A New Technique for Monitoring Movement of Buried Objects Using an Electrode Switching System
Authors: Li Zhihua , Kutter Bruce L. 
Published: March 2008

Abstract
A novel technique for monitoring movement of buried objects using an electrode switching system is developed. The idea is to establish electromagnetic fields in a conductive medium by injecting low-frequency alternating currents through boundary electrodes. The movement of a buried object is related to the electrical potential measured on an electrode attached to it. A closed-form expression for potential distribution in a rectangular container is developed; boundary conditions are accounted for using a method of images. The resolution of spatial location using the proposed electro-location scheme is limited by the electrical noise and the accuracy of potential measurement, which depends on the excitation frequency, measurements per cycle of excitation, and samples per measurement. The tradeoff between spatial and temporal resolution is investigated. With appropriate sampling parameters, spatial and temporal resolutions of 1 mm and 1 ms have been demonstrated. The viability of the electro-location technique is demonstrated by measuring the liquefaction-induced settlements of heavy objects in the geotechnical centrifuge model test using an electrode switching system. The obtained positions agree remarkably with independent measurements. The electro-location method is considered to be a useful technique for monitoring subsurface movements in physical centrifuge models and has practical application potentials in the field.
The Effect of Hydrogen on the Transition Behavior of the Corrosion Rate of Zirconium Alloys
Authors: Harada Makoto , Wakamatsu Ryuji 
Published: March 2008

Abstract
Three zirconium alloys (Zry-4, Zry-2, and NDA) were corrosion tested at 633 K in pure water and in mixed gas of Ar and oxygen. In both environments, their corrosion rate showed cyclic changes. The time and the weight gain at the transition point changed with their corrosion resistance. In the pure water corrosion test, one test cycle was 600 h, and the cumulative total test duration was as much as 7200 h. After each test cycle, the weight changes and the hydrogen contents were analyzed. The hydrogen pick-up ratio was calculated for each test cycle based on the weight change and the increase of the hydrogen content. The calculated hydrogen pick-up ratios were not constant. They showed periodic changes. In the pre-transition region, the corrosion rate showed a gradual decrease; however, the calculated hydrogen pick-up rate gradually increased. After the transition, in contrast to the increase in the corrosion rate, the calculated hydrogen pick-up rate decreased. The changes of the corrosion rate and the calculated hydrogen pick-up rate for the test interval exhibited an inverse relationship. Transmission electron microscopy (TEM), scanning TEM, energy dispersive x-ray (EDX) spectroscopy, and electron diffraction (ED) pattern analysis of the oxide/metal interface showed the existence of an interface layer that consists of distorted ZrO2 and a sub-oxide. Before the transition, the interface layer was clearly observed. On the other hand, the interface layer disappeared after the transition. The cyclic changes in the corrosion rate were closely related to the interface barrier layer at the oxide/metal interface. The interface layer suppresses the corrosion rate, and the degradation of its barrier property increases the corrosion rate. By comparing the morphology of the oxide/metal interface between the water corrosion samples and the mixed gas oxidation samples, it can be seen that the generated hydrogen in the oxide may have two opposite effects. One is to stabilize the interface layer and to suppress the transport of the oxygen ion, and the other is to degrade the interface layer at the transition and accelerate the generation of the uniform oxide. The effect of the chemical composition on the properties of the oxide-metal interface and the mechanism of the corrosion transition will be discussed.
A Study of Thin Coating Wear in High Data Density Tape Heads
Authors: Shi Baogui , Sullivan J. L. , Saied S. O. 
Published: March 2008

Abstract
This paper reports on an investigation of the wear of very thin (20–50 nm) Cr2O3 hard coatings, deposited on the linear tape open (LTO) data tape heads. The differential wear of the magnetic poles on the head and subsequent pole tip recession (PTR) leading to an increase in magnetic spacing is the major factor limiting the performance of high data density data tape heads. In order to reduce or eliminate PTR, very thin Cr2O3 hard coatings were employed to reduce PTR. The coatings were deposited on the LTO heads surface using unbalanced magnetron sputtering deposition techniques. Atomic force microscopy was used to analyze the surface topography of the coated head surface. Wear measurement was carried out by the means X-ray photoelectron spectroscopy and Auger electron spectroscopy combined with argon ion depth profiling. By these means, the very small reduction in coating thickness during the wear and hence the wear rate could be accurately determined. Wear tests were conducted in modified HP LTO Ultrium Generation 1 tape drives, and it is shown that wear rates of below 5.6×10−21m3/N⋅m could be measured. Nano indentation and scratch tests were employed to study the wear of the head materials and coated heads, which indicated that pole materials suffer the greatest wear under the same wear test conditions. The coatings on the pole areas have the lowest anti-abrasive wear resistance. Compared to the uncoated heads, the PTR of LTO heads were significant reduced by Cr2O3 coatings.
Evaluating the Effect of Stressors on Thiaminase Activity in Alewife
Authors: Lepak Jesse M. , Kraft Clifford E. , Honeyfield Dale C. , Brown Scott B. 
Published: March 2008

Abstract
No consistent explanation has been found for the variability in the thiaminase activity of alewives Alosa pseudoharengus despite the role of alewife thiaminase in large-scale salmonine mortality in the Laurentian Great Lakes. We conducted experiments to evaluate the effect of two stressors, reduced salt content in the water and food limitation, on alewife thiaminase activity. Alewives were subjected to treatments in replicated tanks in which conductivity was lowered (&lt;100 μS/cm) for 8 d and feeding was limited for 39 d. Circulating white blood cells, plasma cortisol, plasma glucose, and whole-body thiaminase were measured in individual alewives to assess their response to these experimental treatments. Alewives from the controls had significantly larger numbers of circulating white blood cells than those in the salt-reduced and food-limited treatments (24,000 and 19,000 cells/μL and 11,000 and 9,000 cells/μL for alewives from the two control and salt-reduced treatment tanks, respectively, and 34,000 and 30,000 cells/μL and 21,000 and 16,000 cells/μL for alewives from the two control and food-limited treatment tanks). No significant differences in alewife thiaminase activity were found between treatment fish and their controls. The mean thiaminase activity in the alewives studied increased from 6,900 to 16,000 pmol·g−1·min−1 from the time of their collection in Cayuga Lake to the start of laboratory experiments 1.5–2.5 years later; the latter value was more than twice that of previously reported levels of thiaminase activity from alewives collected in the wild. These data suggest that the variability in alewife thiaminase is not related to stress from salt reduction or food limitation, but laboratory holding conditions significantly increased thiaminase through a mechanism not evaluated by our experimental treatments.
Severity of Barotrauma Influences the Physiological Status, Postrelease Behavior, and Fate of Tournament-Caught Smallmouth Bass
Authors: Gravel Marie-Ange , Cooke Steven J. 
Published: March 2008

Abstract
Much research on the fish physiological consequences of tournaments has been conducted to date and has provided anglers and tournament organizers with strategies for reducing stress and mortality. However, one aspect of tournaments that has received little attention is barotrauma. At a fall competitive angling event on Rainy Lake in northwestern Ontario, we evaluated the incidence of barotrauma among tournament-caught smallmouth bass Micropterus dolomieu; we then tagged and released a subset of fish that had severe barotrauma indicators and compared physiology, postrelease behavior, and fate between these fish and those with negligible signs of barotrauma. Overall, 76% of fish had at least one sign of barotrauma (either hemorrhaging or swim bladder distention), but only 32% of fish had two or more indicators and were thus deemed to have severe barotrauma. When telemetered fish were released at a common site, we determined that fish with negligible signs of barotrauma evacuated the release site more rapidly than fish with severe barotrauma did. Some fish with barotrauma floundered at the surface when released, and one of these fish was subsequently hit and killed by a boat. At the end of the monitoring period, 20% of fish with severe barotrauma had died; two additional individuals (20%) that were still at the release site were moribund (failed to respond to diver stimuli). Conversely, we failed to observe any mortality in fish with negligible signs of barotrauma. All tournament fish had elevated levels of blood glucose and lactate. However, stress indices were higher in fish with barotrauma and tended to be highest among fish with barotrauma that died after release. This study revealed that the incidence of barotrauma in tournaments can be high; moreover, outside of a laboratory environment, a significant proportion of fish with severe barotrauma may die after release. Additional research is needed to determine the seasonal variation in incidence and consequences of barotrauma as well as the effectiveness of different depressurization techniques in the field that could be used during fishing tournaments.
Seasonal Patterns of Terrestrial and Aquatic Prey Abundance and Use byOncorhynchus mykissin a California Coastal Basin with a Mediterranean Climate
Authors: Rundio David E. , Lindley Steven T. 
Published: March 2008

AbstractTerrestrial invertebrates are a major source of prey for salmonids in many streams. Their importance as prey appears to be related to (1) the seasonal timing of terrestrial inputs relative to the abundance of aquatic prey and (2) water temperature, which affects food demand by fish. Most studies of seasonal patterns of terrestrial inputs have come from temperate systems, and patterns in most other systems are unknown. We measured monthly biomass of aquatic invertebrates, input of terrestrial invertebrates, and diets ofOncorhynchus mykiss(non‐anadromous and juvenile anadromous life history forms) for 15 months in two streams in a basin with a Mediterranean‐type climate on the Big Sur coast of California. Biomass of aquatic invertebrates and terrestrial inputs followed a similar seasonal pattern; highest levels occurred in summer and early autumn and were highly correlated with water temperature. Total annual input of terrestrial invertebrates was 8.7 g·m−2·year−1, and terrestrial inputs provided about half of the prey biomass and energy consumed byO. mykissduring the study. Nonnative terrestrial isopods, primarilyArmadillidium vulgare, contributed 30‐40% of the biomass and 20‐30% of the energy consumed—the highest proportions among all taxa. The annual input, seasonal pattern, and contribution of terrestrial invertebrates to salmonids in this coastal Mediterranean‐type basin were similar to published values from temperate forested streams. However, the magnitude of seasonal fluctuations of inputs was less pronounced than that in most temperate streams and appears to reflect the lower intra‐annual temperature variation and longer leaf‐out period in this system. Unlike many temperate streams, where terrestrial inputs provide an alternate prey source when aquatic invertebrate abundance is low, terrestrial inputs to these two coastal streams apparently provide a year‐round additional source of prey that (like aquatic prey) peaks when water temperature is warmest and hence when fish growth potential is high.
Depth of Processing in Private and Social Speech: Its Role in the Retention of Word Knowledge by Adult EAP Learners
Authors: Borer Linda 
Published: March 2008

Abstract: This study explored the effect on vocabulary retention of vocalizations involving three cognitive processing depths (repetition, manipulation, and generation). Eight participants in an English for academic purposes (EAP) context encountered five unknown words when working alone and five different words when working in pairs. In each condition, they studied the words from a text and dictionary, completed puzzle and question tasks, and did a stimulated recall. Tests one week and one month later assessed short- and long-term retention. The data were examined to investigate whether vocalization of deeper processing was associated with better retention, how deeper processing facilitated matches between task utterances and test responses, and which condition (solitary or collaborative) produced higher test scores. Quantitative results show that delayed test scores correlated inversely with repetition during collaboration. Qualitative analysis suggests that vocalizations were better remembered when participants deployed deeper processing to create mnemonics, connect input with L1/L2 knowledge, and express opinions. Solitary and collaborative conditions were equally effective in promoting retention.