bluuebunny/crossref_metadata_2025_split huggingface dataset:
Real wave packet and flux analysis studies of the H + F2 → HF + F reaction
Authors: Gogtas Fahrettin , Karabulut Ezman , Tanaka Tomokazu , Takayanagi Toshiyuki , Tutuk Rukiye 
Published: August 2011

AbstractThe H + F2 → HF + F reaction on ground state potential energy surface is investigated using the quantum mechanical real wave packet and Flux analysis method based on centrifugal sudden approximation. The initial state selected reaction probabilities for total angular momentum J = 0 have been calculated by both methods while the probabilities for J > 0 have been calculated by Flux analysis method. The initial state selected reaction probabilities, integral cross sections and rate coefficients have been calculated for a broad range of collision energy. The results show a large rotational enhancement of the reaction probability. Some resonances were seen in the state‐to‐state reaction probabilities while state‐to‐all reaction probabilities and the reaction cross section do not manifest any oscillations and the initial state selected reaction rate constants are sensitive to the temperature. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
Effects of perinatal asphyxia on rat striatal cytoskeleton
Authors: Saraceno G.E. , Ayala M.V. , Badorrey M.S. , Holubiec M. , Romero J.I. , Galeano P. , Barreto G. , Giraldez‐Alvárez L.D. , Kölliker‐fres R. , Coirini H. , Capani F. 
Published: August 2011

AbstractPerinatal asphyxia (PA) is a medical condition associated with a high short‐term morbimortality and different long‐term neurological diseases. In previous works, we have shown that neuronal and synaptic changes in rat striatum lead to ubi‐protein accumulation in post‐synaptic density (PSD) after six months of sub‐severe PA. However, very little is known about the synaptic and related structural modifications induced by PA in young rats. In the present work, we studied neuronal cytoskeleton modifications in striatum induced by subsevere PA in 30‐day‐old rats. We observed a significant decrease in the number of neurons, in particular calbindin immunoreactive neurons after PA. In addition, it was also observed that actin cytoskeleton was highly modified in the PSD as well as an increment of F‐actin staining by Phalloidin‐alexa488 in the striatum of PA rats. Using correlative fluorescence‐electron microscopy photooxidation, we confirmed and extended confocal observations. F‐actin staining augmentation was mostly related with an increment in the number of mushroom‐shaped spines. Consistent with microscopic data, Western blot analysis revealed a β‐actin increment in PSD in PA rats. On the other hand, MAP‐2 immunostaining was decreased after PA, being NF‐200 expression unmodified. Although neuronal death was observed, signs of generalized neurodegeneration were absent. Taken together these results showed early post‐synaptic F‐actin cytoskeleton changes induced by PA with slightly modifications in the other components of the neuronal cytoskeleton, suggesting that F‐actin accumulation in the dendritic spines could be involved in the neuronal loss induced by PA. Synapse, 2012. © 2011 Wiley Periodicals, Inc.
Evolutionary computation for training set selection
Authors: García‐Pedrajas Nicolás 
Published: August 2011

AbstractInstance selection is becoming increasingly relevant because of the large amount of data that is constantly being produced in many fields of research. Two basic approaches exist for instance selection: instance selection as a method for prototype selection for instance‐based methods (such as k‐nearest neighbors) and instance selection for obtaining the training set for classifiers that require a learning process (such as decision trees or neural networks). In this paper, we review the methods that have been developed thus far for the latter approach within the field of evolutionary computation. Different groups of learning algorithms require different instance selectors to suit their learning/search biases. This requirement may render many instance selection algorithms useless if their philosophy of design is not suitable for the problem at hand. Evolutionary algorithms do not assume any structure of the data or any behavior of the classifier but instead adapt the instance selection to the performance of the classifier. They are therefore very suitable for training set selection. The main algorithms that have been developed for decision trees, artificial neural networks, and other classifiers are presented. We also discuss the relevant issue of the scalability of these methods to very large datasets. Although current algorithms are useful for fairly large datasets, scaling problems are found when the number of instances is in the hundreds of thousands or millions. © 2011 John Wiley & Sons, Inc. WIREs Data Mining Knowl Discov 2011 1 512–523 DOI: 10.1002/widm.44This article is categorized under:

Technologies > Computational Intelligence
Technologies > Computer Architectures for Data Mining
Technologies > Data Preprocessing
Monitoring the gestation period of rescued Formosan pangolin (Manis pentadactyla pentadactyla) with progesterone radioimmunoassay
Authors: Chin Shih‐Chien , Lien Chen‐Yen , Chan Ya‐Ting , Chen Chun‐Lin , Yang Yi‐Ching , Yeh Lih‐Seng 
Published: August 2011

AbstractEight species of pangolin have been identified in the world. However, understanding of pangolin reproductive biology has been limited to fragmentary records. In this study, the concentration of serum progesterone in three pregnant and two nonpregnant rescued female Formosan pangolins (Manis pentadactyla pentadactyla) was monitored using a commercial progesterone radioimmunoassay kit. During gestation, the serum progesterone of pregnant pangolins A, B, and C remained at 28.5–55 ng/ml (n = 31 samples), 10.9–50.1 ng/ml (n = 34), and 12.4 and 33.5 ng/ml with a peak at 47.6 ng/ml (n = 19), respectively, whereas the serum progesterone of nonpregnant pangolins D and E remained at 1.99 ± 1.62 ng/ml (n = 80) and 2.27 ± 1.64 ng/ml (n = 27), respectively. From this study, it was found that female pangolin weighing as low as 2.14 kg was already capable of reproduction. For pregnant pangolins to give birth to viable offspring, their body weight must increase significantly, 63.89 and 134.0% in the study, from the time of inception or early pregnancy until parturition. In addition, study has found that both viable offspring were born fully developed and exceeded 80 g in weight. The period of gestation was found to be as short as 318 or longer than 372 days. Therefore, the Formosan pangolin should only be able to reproduce once a year. This study is the first insight into hormone assay for determining the gestation period of pangolin. Further investigations on the same subject are necessary to establish criteria for the recognition of reproductive status in pangolins. Zoo Biol 31:479–489, 2012. © 2011 Wiley Periodicals, Inc.
Resting orientation enhances prey survival on strongly structured background
Authors: Wang Zhen , Schaefer H. Martin 
Published: August 2011

AbstractPrey can use various camouflage types as defense against predators. One of the most common and important types is background matching, which occurs if an animal matches the background in color, brightness, and pattern. Although background matching has been studied intensively, the effects of the resting orientation of prey on the effectiveness of camouflage through background matching are not well known in natural conditions. Several past experimental studies have been conducted on resting orientation in the lab often using the visual system of humans. Their results revealed that the detection rates of predators hinge on the combination of the resting orientation of artificial moths and their background. Here, we studied whether survival rates of artificial moth‐like models depend on their resting orientation in the wild where the visual conditions and detection distances vary. We used a 2 × 2 design of two resting positions of a horizontally and a vertically striped morph on tree bark. Our results show that the survival probability of moths depended mainly on the orientation of stripes relative to the vertical structure of tree bark. Thus, resting orientation relative to background affected survival. After reanalyzing Endler's (Biol J Linn Soc 22:187–231, 1984) data on resting habitats of 317 species of North American moths, we found that horizontally striped moths occurred frequently on small herbs and tree bark. We suggest that it would be beneficial for striped moths to orient non‐randomly on strongly structured background, like furrows of tree bark. We further suggest that background matching was more important than coincident disruptive coloration in determining the survival rates of our artificial moths.
Ejaculatory dysfunction as a cause of infertility
Authors: Kondoh Nobuyuki 
Published: August 2011

AbstractEjaculatory dysfunction (EjD), the most prevalent male sexual disorder, is clearly different from erectile dysfunction (ED). EjD is divided into 4 categories: premature ejaculation, delayed ejaculation, retrograde ejaculation and anejaculation. EjD‐related infertility is one of the most serious problems in young patients. If sexual intercourse is achieved successfully without any ejaculate sexual partners/wives will not be able to conceive. Therefore, establishment of management of EjD as well as ED is increasingly crucial for couples wishing for a baby. The therapeutic approach of EjD‐related infertility is based upon two scenarios: (1) if EjD alone is the reason for having no children, adequate treatment for EjD alone is required, or (2) if EjD is not the only reason and is combined with a worsening of semen quality, total management for male infertility (including EjD treatment) is needed. In this article, the background of EjD‐related infertility is presented briefly, followed by a review of treatment modalities.
Problems of Oxfordian and Kimmeridgian stratigraphy in northern Central Siberia (Nordvik Peninsula section)
Authors: Nikitenko B.L. , Knyazev V.G. , Lebedeva N.K. , Peshchevitskaya E.B. , Kutygin R.V. 
Published: August 2011

Abstract
The Oxfordian–Lower Hauterivian section of the Nordvik Peninsula (northern Central Siberia) is a reference for developing zonal scales for various fossil groups and improving the Boreal zonal standard. In the middle 1950s–late 1980s, it was studied extensively by geologists, stratigraphers, lithologists, and experts on various fossil groups. These studies yielded rich fossil and microfossil collections and a set of parallel zonal scales for various faunal groups. Recently, a new detailed ammonite zonation of the Oxfordian and Kimmeridgian units of this section has been proposed. These results contradict the previous biostratigraphic data on ammonites, foraminifers, and palynomorphs. In the present paper, all the biostratigraphic data on the Oxfordian and Kimmeridgian units of the Nordvik Peninsula (Cape Urdyuk-Khaya) and northern Central Siberia undergo a comprehensive analysis and comparison with those on the Boreal Realm. The ammonite-constrained stratigraphic position of the lower Upper Jurassic in the Cape Urdyuk-Khaya section is interpreted as Upper Oxfordian or Middle Oxfordian. In our view, this difference in the understanding is due to the misidentification of some Oxfordian ammonite forms. The zones based on other fossil groups (foraminifers, dinocysts) which were distinguished in the Upper Oxfordian and Kimmeridgian sections of the Nordvik Peninsula are well traceable circumarctically. Their stratigraphic position in various regions of the Northern Hemisphere is constrained by ammonites and bivalves. However, if we use the last alternative ammonite zonation of this section part, hardly explicable contradictions will appear in interregional foraminiferal and dinocyst correlations.
Tectonic interpretation of the thermochronological data and PT-conditions of rock metamorphism in the Bodonchin zonal complex (Mongolian Altay)
Authors: Polyansky O.P. , Sukhorukov V.P. , Travin A.V. , Alekhin I.G. , Yudin D.S. 
Published: August 2011

Abstract
Based on the new petrological and thermochronological data, analysis of the metamorphism conditions and tectonic evolution of the Bodonchin zonal complex in the Mongolian Altay was performed. Using mineral geothermometers and geobarometers, the parameters of the thermal state of the Mongolian Altay crust site during the collision of terranes were estimated, and the paleogeotherm at the peak of syncollisional metamorphism was reconstructed. The thermal state of the crust was determined by either a high concentration of radioactive heat sources or a high mantle heat flow. The estimated metamorphism temperatures and pressures of rocks in two zones (staurolite-kyanite schists and migmatites) of the Bodonchin complex correspond to the paleogeotherms with average temperature gradients ∂T/∂z = 25.5 and 27.2 ºC/km. The results of isotope dating of zircons and metamorphic minerals were used to construct a thermochronological model for the regressive stage of evolution of the polymetamorphic complex. The rates of the ascent of metamorphic rocks to the surface as a result of thrusts in the Bulgan Fault zone were estimated at 0.3–1 mm/year.
Linear microstability analysis of a low-Z impurity doped tokamak plasma
Authors: Romanelli M. , Szepesi G. , Peeters A.G. , Apicella M.L. , Marinucci M. , Mazzotta C. , Mazzitelli G. , Frigione D. 
Published: August 2011

Improved electron and deuterium energy and particle confinement in the presence of low-Z impurities have been observed in many tokamaks under various experimental conditions. Peaked electron density profiles have been obtained in the Frascati Tokamak Upgrade (FTU) ohmic plasmas where a high concentration of lithium has been detected following the installation of a Liquid Lithium Limiter (LLL). This paper presents the results of a gyrokinetic study on the effects of lithium and other low-Z impurities on the linear stability of deuterium and electron temperature driven modes and their associated fluxes for plasma parameters such as those found in the core of LLL-FTU plasmas.
Simulations show that a lithium concentration in excess of n
Li/n
e = 15%, as estimated in the initial phase of a reference FTU discharge, is found to have a strong stabilizing effect on the TEM and high-frequency ETG modes. A significant stabilization of the electron driven modes can still be observed when the lithium concentration is reduced to 3%.
In the presence of a significant impurity concentration (n
Li/n
e = 3–15%) the long wavelength ITG modes drive an inward electron and deuterium flux and outward lithium flux. This process may lead eventually to an increased electron and deuterium density peaking and a reduced Z
eff (lithium density below n
Li/n
e = 1%).
Comparative analysis of algorithms for next-generation sequencing read alignment
Authors: Ruffalo Matthew , LaFramboise Thomas , Koyutürk Mehmet 
Published: August 2011

Abstract
Motivation: The advent of next-generation sequencing (NGS) techniques presents many novel opportunities for many applications in life sciences. The vast number of short reads produced by these techniques, however, pose significant computational challenges. The first step in many types of genomic analysis is the mapping of short reads to a reference genome, and several groups have developed dedicated algorithms and software packages to perform this function. As the developers of these packages optimize their algorithms with respect to various considerations, the relative merits of different software packages remain unclear. However, for scientists who generate and use NGS data for their specific research projects, an important consideration is choosing the software that is most suitable for their application.
Results: With a view to comparing existing short read alignment software, we develop a simulation and evaluation suite, Seal, which simulates NGS runs for different configurations of various factors, including sequencing error, indels and coverage. We also develop criteria to compare the performances of software with disparate output structure (e.g. some packages return a single alignment while some return multiple possible alignments). Using these criteria, we comprehensively evaluate the performances of Bowtie, BWA, mr- and mrsFAST, Novoalign, SHRiMP and SOAPv2, with regard to accuracy and runtime.
Conclusion: We expect that the results presented here will be useful to investigators in choosing the alignment software that is most suitable for their specific research aims. Our results also provide insights into the factors that should be considered to use alignment results effectively. Seal can also be used to evaluate the performance of algorithms that use deep sequencing data for various purposes (e.g. identification of genomic variants).
Availability: Seal is available as open source at http://compbio.case.edu/seal/.
Contact: matthew.ruffalo@case.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Detecting biological network organization and functional gene orthologs
Authors: Cui Jike , DeLuca Todd F. , Jung Jae-Yoon , Wall Dennis P. 
Published: August 2011

Abstract
SUMMARY: We developed a package TripletSearch to compute relationships within triplets of genes based on Roundup, an orthologous gene database containing &gt;1500 genomes. These relationships, derived from the coevolution of genes, provide valuable information in the detection of biological network organization from the local to the system level, in the inference of protein functions and in the identification of functional orthologs. To run the computation, users need to provide the GI IDs of the genes of interest.
Availability: http://wall.hms.harvard.edu/sites/default/files/tripletSearch.tar.gz
Contact: dpwall@hms.harvard.edu
Supplementary Information: Supplementary data are available at Bioinformatics online.
Vacuolar Transport in Tobacco Leaf Epidermis Cells Involves a Single Route for Soluble Cargo and Multiple Routes for Membrane Cargo
Authors: Bottanelli Francesca , Foresti Ombretta , Hanton Sally , Denecke Jürgen 
Published: August 2011

AbstractWe tested if different classes of vacuolar cargo reach the vacuole via distinct mechanisms by interference at multiple steps along the transport route. We show that nucleotide-free mutants of low molecular weight GTPases, including Rab11, the Rab5 members Rha1 and Ara6, and the tonoplast-resident Rab7, caused induced secretion of both lytic and storage vacuolar cargo. In situ analysis in leaf epidermis cells indicates a sequential action of Rab11, Rab5, and Rab7 GTPases. Compared with Rab5 members, mutant Rab11 mediates an early transport defect interfering with the arrival of cargo at prevacuoles, while mutant Rab7 inhibits the final delivery to the vacuole and increases cargo levels in prevacuoles. In contrast with soluble cargo, membrane cargo may follow different routes. Tonoplast targeting of an α-TIP chimera was impaired by nucleotide-free Rha1, Ara6, and Rab7 similar to soluble cargo. By contrast, the tail-anchored tonoplast SNARE Vam3 shares only the Rab7-mediated vacuolar deposition step. The most marked difference was observed for the calcineurin binding protein CBL6, which was insensitive to all Rab mutants tested. Unlike soluble cargo, α-TIP and Vam3, CBL6 transport to the vacuole was COPII independent. The results indicate that soluble vacuolar proteins follow a single route to vacuoles, while membrane spanning proteins may use at least three different transport mechanisms.
Conservation and Purifying Selection of Transcribed Genes Located in a Rice Centromere
Authors: Fan Chuanzhu , Walling Jason G. , Zhang Jianwei , Hirsch Cory D. , Jiang Jiming , Wing Rod A. 
Published: August 2011

AbstractRecombination is strongly suppressed in centromeric regions. In chromosomal regions with suppressed recombination, deleterious mutations can easily accumulate and cause degeneration of genes and genomes. Surprisingly, the centromere of chromosome8 (Cen8) of rice (Oryza sativa) contains several transcribed genes. However, it remains unclear as to what selective forces drive the evolution and existence of transcribed genes in Cen8. Sequencing of orthologous Cen8 regions from two additional Oryza species, Oryza glaberrima and Oryza brachyantha, which diverged from O. sativa 1 and 10 million years ago, respectively, revealed a set of seven transcribed Cen8 genes conserved across all three species. Chromatin immunoprecipitation analysis with the centromere-specific histone CENH3 confirmed that the sequenced orthologous regions are part of the functional centromere. All seven Cen8 genes have undergone purifying selection, representing a striking phenomenon of active gene survival within a recombination-free zone over a long evolutionary time. The coding sequences of the Cen8 genes showed sequence divergence and mutation rates that were significantly reduced from those of genes located on the chromosome arms. This suggests that Oryza has a mechanism to maintain the fidelity and functionality of Cen8 genes, even when embedded in a sea of repetitive sequences and transposable elements.
Combined Noninvasive Imaging and Modeling Approaches Reveal Metabolic Compartmentation in the Barley Endosperm
Authors: Rolletschek Hardy , Melkus Gerd , Grafahrend-Belau Eva , Fuchs Johannes , Heinzel Nicolas , Schreiber Falk , Jakob Peter M. , Borisjuk Ljudmilla 
Published: August 2011

AbstractThe starchy endosperm of cereals is a priori taken as a metabolically uniform tissue. By applying a noninvasive assay based on 13C/1H-magnetic resonance imaging (MRI) to barley (Hordeum vulgare) grains, we uncovered metabolic compartmentation in the endosperm. 13C-Suc feeding during grain filling showed that the primary site of Ala synthesis was the central region of the endosperm, the part of the caryopsis experiencing the highest level of hypoxia. Region-specific metabolism in the endosperm was characterized by flux balance analysis (FBA) and metabolite profiling. FBA predicts that in the central region of the endosperm, the tricarboxylic acid cycle shifts to a noncyclic mode, accompanied by elevated glycolytic flux and the accumulation of Ala. The metabolic compartmentation within the endosperm is advantageous for the grain's carbon and energy economy, with a prominent role being played by Ala aminotransferase. An investigation of caryopses with a genetically perturbed tissue pattern demonstrated that Ala accumulation is a consequence of oxygen status, rather than being either tissue specific or dependent on the supply of Suc. Hence the 13C-Ala gradient can be used as an in vivo marker for hypoxia. The combination of MRI and metabolic modeling offers opportunities for the noninvasive analysis of metabolic compartmentation in plants.