bluuebunny/crossref_metadata_2025 huggingface dataset:
HOMOLOGOUS SYNTENY BLOCK DETECTION BASED ON SUFFIX TREE ALGORITHMS
Authors: CHEN YU-LUN , CHEN CHIEN-MING , PAI TUN-WEN , LEONG HON-WAI , CHONG KET-FAH
Published: October 2013

A synteny block represents a set of contiguous genes located within the same chromosome and well conserved among various species. Through long evolutionary processes and genome rearrangement events, large numbers of synteny blocks remain highly conserved across multiple species. Understanding distribution of conserved gene blocks facilitates evolutionary biologists to trace the diversity of life, and it also plays an important role for orthologous gene detection and gene annotation in the genomic era. In this work, we focus on collinear synteny detection in which the order of genes is required and well conserved among multiple species. To achieve this goal, the suffix tree based algorithms for efficiently identifying homologous synteny blocks was proposed. The traditional suffix tree algorithm was modified by considering a chromosome as a string and each gene in a chromosome is encoded as a symbol character. Hence, a suffix tree can be built for different query chromosomes from various species. We can then efficiently search for conserved synteny blocks that are modeled as overlapped contiguous edges in our suffix tree. In addition, we defined a novel Synteny Block Conserved Index (SBCI) to evaluate the relationship of synteny block distribution between two species, and which could be applied as an evolutionary indicator for constructing a phylogenetic tree from multiple species instead of performing large computational requirements through whole genome sequence alignment.
COFACTOR MODIFICATION ANALYSIS: A COMPUTATIONAL FRAMEWORK TO IDENTIFY COFACTOR SPECIFICITY ENGINEERING TARGETS FOR STRAIN IMPROVEMENT
Authors: LAKSHMANAN MEIYAPPAN , CHUNG BEVAN KAI-SHENG , LIU CHENGCHENG , KIM SEON-WON , LEE DONG-YUP
Published: October 2013

Cofactors, such as NAD(H) and NADP(H), play important roles in energy transfer within the cells by providing the necessary redox carriers for a myriad of metabolic reactions, both anabolic and catabolic. Thus, it is crucial to establish the overall cellular redox balance for achieving the desired cellular physiology. Of several methods to manipulate the intracellular cofactor regeneration rates, altering the cofactor specificity of a particular enzyme is a promising one. However, the identification of relevant enzyme targets for such cofactor specificity engineering (CSE) is often very difficult and labor intensive. Therefore, it is necessary to develop more systematic approaches to find the cofactor engineering targets for strain improvement. Presented herein is a novel mathematical framework, cofactor modification analysis (CMA), developed based on the well-established constraints-based flux analysis, for the systematic identification of suitable CSE targets while exploring the global metabolic effects. The CMA algorithm was applied to E. coli using its genome-scale metabolic model, iJO1366, thereby identifying the growth-coupled cofactor engineering targets for overproducing four of its native products: acetate, formate, ethanol, and lactate, and three non-native products: 1-butanol, 1,4-butanediol, and 1,3-propanediol. Notably, among several target candidates for cofactor engineering, glyceraldehyde-3-phosphate dehydrogenase (GAPD) is the most promising enzyme; its cofactor modification enhanced both the desired product and biomass yields significantly. Finally, given the identified target, we further discussed potential mutational strategies for modifying cofactor specificity of GAPD in E. coli as suggested by in silico protein docking experiments.
AUTOMATIC PHYLOGENETIC CLASSIFICATION OF BACTERIAL BETA-LACTAMASE SEQUENCES INCLUDING STRUCTURAL AND ANTIBIOTIC SUBSTRATE PREFERENCE INFORMATION
Authors: MA JIANMIN , EISENHABER FRANK , MAURER-STROH SEBASTIAN
Published: October 2013

Beta lactams comprise the largest and still most effective group of antibiotics, but bacteria can gain resistance through different beta lactamases that can degrade these antibiotics. We developed a user friendly tree building web server that allows users to assign beta lactamase sequences to their respective molecular classes and subclasses. Further clinically relevant information includes if the gene is typically chromosomal or transferable through plasmids as well as listing the antibiotics which the most closely related reference sequences are known to target and cause resistance against. This web server can automatically build three phylogenetic trees: the first tree with closely related sequences from a Tachyon search against the NCBI nr database, the second tree with curated reference beta lactamase sequences, and the third tree built specifically from substrate binding pocket residues of the curated reference beta lactamase sequences. We show that the latter is better suited to recover antibiotic substrate assignments through nearest neighbor annotation transfer. The users can also choose to build a structural model for the query sequence and view the binding pocket residues of their query relative to other beta lactamases in the sequence alignment as well as in the 3D structure relative to bound antibiotics. This web server is freely available at http://blac.bii.a-star.edu.sg/ .
HYSTERETIC CHARACTERISTIC WITH P-Δ EFFECT AND ITS INFLUENCE ON COLLAPSE RESISTANCE CAPACITY OF STRUCTURE UNDER EARTHQUAKES
Authors: LIANG RENJIE , WU JING , GE HANBIN , WANG CHUNLIN
Published: October 2013

P-Δ effect is one of the crucial reasons causing the collapse of structures under strong earthquake excitations. Numerical example shows that the lateral stiffness of structure decreases when the P-Δ effect is considered, and the backbone curve is easy to behave a negative slope when the geometric nonlinearity and the material nonlinearity are combined. A simplified trilinear curve including the elastic range, the yield range and the softening range is used to simulate the characteristic of the backbone curve, and the hysteretic models including the nonlinear elastic model, the full elasto-plastic model and the Clough model are developed. The influence of the hysteretic characteristic on the collapse resistance capacity of the structure is researched by a series of incremental dynamic analysis (IDA) for the single-degree-of-freedom (SDOF) system. The results demonstrate that the collapse resistance capacity of the structure is not always proportional to the energy dissipation capacity, while the biasing movement tendency when the structure goes into the negative stiffness branch is the main reason causing the collapse of the structure.
MESOSCALE MODELING OF CONCRETE UNDER DYNAMIC SPLIT TENSION
Authors: ZHOU XIAO-QING , XIA YONG
Published: October 2013

In this paper, a mesoscale model is adopted to simulate concrete behavior under dynamic split tension. The concrete material is assumed to comprise coarse aggregates, mortar matrix, and an interfacial transition zone (ITZ). In the mesh generation process, random coarse aggregate particles are generated from a certain aggregate size distribution and then placed into the mortar matrix with ITZ between the coarse aggregate edge and the mortar matrix. Different aggregate shapes, such as circular, oval, and polygons are modeled to analyze the gravel and crushed stone aggregates. Numerical simulation is used to model the dynamic damage responses of a typical cylinder concrete specimen and a cube specimen under split tension. Velocity boundary is added as the dynamic loading. Reasonable tensile stress–strain relationships are obtained at the macroscale level; and the detailed stress wave distribution and the crack pattern are obtained at the mesoscale level. These numerical results agree well with conventional experimental results. It also shows that cracks are affected by aggregate distribution.
Optical coherence tomography of the living human kidney
Authors: Andrews Peter M. , Wang Hsing-Wen , Wierwille Jeremiah , Gong Wei , Verbesey Jennifer , Cooper Matthew , Chen Yu
Published: October 2013

Acute tubular necrosis (ATN) induced by ischemia is the most common insult to donor kidneys destined for transplantation. ATN results from swelling and subsequent damage to cells lining the kidney tubules. In this study, we demonstrate the capability of optical coherence tomography (OCT) to image the renal microstructures of living human donor kidneys and potentially provide a measure to determine the extent of ATN. We also found that Doppler-based OCT (i.e., DOCT) reveals renal blood flow dynamics that is another major factor which could relate to post-transplant renal function. All OCT/DOCT observations were performed in a noninvasive, sterile and timely manner on intact human kidneys both prior to (ex vivo) and following (in vivo) their transplantation. Our results indicate that this imaging model provides transplant surgeons with an objective visualization of the transplant kidneys prior and immediately post transplantation.
CENTRAL LIMIT THEOREM FOR LINEAR STATISTICS OF EIGENVALUES OF BAND RANDOM MATRICES
Authors: LI LINGYUN , SOSHNIKOV ALEXANDER
Published: October 2013

We prove the Central Limit Theorem for linear statistics of the eigenvalues of band random matrices provided [Formula: see text] and test functions are sufficiently smooth.
Chapter 11 Geology, volcanic history and petrology of Vulcano (central Aeolian archipelago)
Authors: De Astis G. , Lucchi F. , Dellino P. , La Volpe L. , Tranne C. A. , Frezzotti M. L. , Peccerillo A.
Published: October 2013

Vulcano is an active NW–SE-elongated composite volcano located in the central Aeolian archipelago. Based on available radiometric ages and tephrochronology, the exposed volcanism started at
c.
127 ka and spread through eight Eruptive Epochs separated by volcano-tectonic events and major quiescent stages. Various eruptive centres and two intersecting multi-stage calderas resulted from such evolution. Vulcano geological history displays several changes of eruption magnitude, eruption styles and composition of magmas through time. Vulcano rocks range from basalt to rhyolite and show variable alkali contents, roughly increasing during time. Magmas with low to intermediate SiO
2
contents and high-K to shoshonite affinity prevail in the early Epochs 1–5 (
c.
127–28 ka), whereas intermediate to high-SiO
2
shoshonite and potassic alkaline products dominate the last three Epochs (<30 ka). This sharp increase in silicic products is related to the shallowing of the plumbing system and resulting major role of the differentiation processes in shallow-level reservoirs. Radiogenic isotope compositions are variable (
87
Sr/
86
Sr=0.70424–0.70587,
143
Nd/
144
Nd=0.51254–0.51276,
206
Pb/
204
Pb=19.305–19.759,
207
Pb/
204
Pb=15.659–15.752,
208
Pb/
204
Pb=39.208–39.559) as a result of both source heterogeneities and shallow-level interaction of magmas with continental crust. The compositional variations of mafic magmatism with time suggest that the source zone changed from a metasomatized, fertile, ocean island basalt- (OIB-) like mantle to a metasomatized depleted lithospheric mantle.

DVD:

The 10 000 scale geological map of Vulcano is included on the DVD in the printed book and can also be accessed online at
http://www.geolsoc.org.uk/Memoir37-electronic
. Also included is a full geochemical data set for Vulcano.
Chapter 12 Geological history of the Panarea volcanic group (eastern Aeolian archipelago)
Authors: Lucchi F. , Tranne C. A. , Peccerillo A. , Keller J. , Rossi P. L.
Published: October 2013

The Panarea volcanic group is made up of dome-fields that are the subaerial culminations of a largely dissected volcanic complex mostly located below sea level. The correlation of marine isotope stage (MIS) 5 marine terrace deposits and numerous tephra layers, combined with the available radiometric ages, shows that the Panarea dome-fields mostly developed between
c.
155–149 and 124–118 ka through the emplacement of successive lava domes, lava flows and minor pyroclastic products, interrupted by dormant periods and episodes of faulting in a context of regional uplift, plus volcano-related deformation. Recurrent explosive phases subsequently occurred in the area of minor islets at
c.
100 ka (Punta Falcone), 67–56 ka (p
1
) and 24–8.7 ka (Drauto), together with the emission of the
c.
54 ka Basiluzzo dome. The Panarea volcanic group is presently in a quiescent state with fumarolic activity and episodic gas outbursts. Panarea rocks show basaltic andesite and high-K basaltic andesite to high-K dacite and rhyolite compositions, with minor shoshonites. Radiogenic isotope signatures range between those typical of the western Aeolian islands and Stromboli. This reveals a heterogeneous mantle source, which resulted from migration of more primitive asthenospheric mantle from the west during slab rollback, and its admixture with more strongly contaminated Stromboli-type resident mantle.

DVD:

The 10 000 scale geological map of Panarea is included on the DVD in the printed book and can also be accessed online at
http://www.geolsoc.org.uk/Memoir37-electronic
. Also included is a full geochemical data set for the Panarea volcanic group.
Chapter 2 Kinematics of the Aeolian volcanism (Southern Tyrrhenian Sea) from geophysical and geological data
Authors: Ventura Guido
Published: October 2013

The Aeolian volcanism (
c.
1 Ma active) develops within the Africa–Eurasia convergence setting, which is characterized by the subduction of the Ionian plate below the Calabrian Arc. Deep earthquakes occur to the east of a tear fault that divides the Aeolian Islands into two sectors: (a) an eastern sector characterized by active volcanism, reduced crustal thickness, high seismic flux, low P-wave velocity (Vp) and attenuation (Qp) and NE–SW extension; (b) a western sector where a NNW–SSE compressive strain along a WNW–ESE-striking fault system is acting. The geophysical and structural features of the eastern sector are consistent with upwelling and SE migration of the asthenospheric mantle. The extensional and strike-slip strain allow the magma to upraise along dyke-like conduits and to erupt. Earthquake-induced strain changes may trigger volcanic eruptions and degassing episodes. The oldest volcanism (Pliocene–Early Pleistocene) was controlled by a WNW–ESE-striking tear fault related to the SE rollback of the slab. A new tear, the Tindari–Letojanni Fault System, started during the Middle–Late Pleistocene and represents the active western boundary of the subducting slab. The present-day Aeolian volcanism is associated with rifting processes developing within an arc collision zone.
Chapter 5 Stratigraphic methodology for the geological mapping of volcanic areas: insights from the Aeolian archipelago (southern Italy)
Authors: Lucchi F.
Published: October 2013

A stratigraphic approach to geological fieldwork and mapping of the Aeolian archipelago is performed by primarily using unconformity-bounded units (UBUs) in addition to lithosomes and classical lithostratigraphic units, which are the basic mappable units. Lithosomes are largely used to identify the localization of eruptive vents or non-volcanic source areas through time. The UBUs display an encompassing framework of correlation on a scale from local (single islands) to regional (Aeolian archipelago), by placing particular emphasis on the stratigraphic role played by Late Quaternary marine terrace deposits and widespread tephra layers (e.g. Brown Tuffs). By establishing a direct relationship between UBUs and time-stratigraphic units, the volcanic successions are readable in terms of different and successive Eruptive Epochs (separated by prolonged non-volcanic periods), which are characterized by distinctive eruptive vents and eruption types. As such, the UBUs allow the reconstruction of the main steps of geological evolution of a volcano as the result of the interplay between volcanic activity of local and external provenance, sea-level fluctuations and volcano-tectonic or regional fault lineaments.
Chapter 7 Volcanism, calderas and magmas of the Alicudi composite volcano (western Aeolian archipelago)
Authors: Lucchi F. , Peccerillo A. , Tranne C. A. , Rossi P. L. , Frezzotti M. L. , Donati C.
Published: October 2013

The Alicudi composite volcano (western Aeolian archipelago) was constructed between
c.
106 and 28 ka by lava flows, domes and strombolian scoriae erupted during six Eruptive Epochs, interrupted by periods of dormancy and three caldera-type collapses in the summit area. Marine Isotope Stage (MIS) 5a (81 ka) terrace deposits and widespread Brown Tuffs of external origin are recognized and provide important marker beds for regional stratigraphic correlations. Volcanism was of central type, under control of the summit caldera collapses with negligible influence of regional tectonic trends. Alicudi rocks are basaltic to high-K andesitic and have the most primitive petrological compositions (high MgO, Ni, Cr contents), the lowest Sr–O and the highest Nd–He isotope ratios (
87
Sr/
86
Sr=0.70352 to 0.70410;
143
Nd/
144
Nd=0.51289 to 0.51279; δ
18
O=+5.0 to 5.6;
3
He/
4
He–R/Ra=
c.
6.5 to 7.1) over the entire Aeolian archipelago. Their composition and variation through time are the result of polybaric crystal–liquid fractionation of parental calc-alkaline basalts to give basaltic andesitic and andesitic derivative melts. These underwent crustal assimilation during ascent, with basalts being contaminated more strongly than andesitic magmas. Sr–Nd–Pb isotopes suggest source metasomatic modification by fluids from an oceanic-type slab, with a minor role for subducted sediments.

DVD:

The 10 000 scale geological map of Alicudi is included on the DVD in the printed book and can also be accessed online at
http://www.geolsoc.org.uk/Memoir37-electronic
. Also included is a geochemical dataset for Alicudi.
Cardiovascular Risk and Hippocampal Thickness in Alzheimer’s Disease
Authors: Donix Markus , Scharf Maria , Marschner Kira , Werner Annett , Sauer Cathrin , Gerner Antje , Nees Josef A. , Meyer Shirin , Donix Katharina L. , Von Kummer Rüdiger , Holthoff Vjera A.
Published: October 2013

Cardiovascular risk factors influence onset and progression of Alzheimer’s disease. Among cognitively healthy people, changes in brain structure and function associated with high blood pressure, diabetes, or other vascular risks suggest differential regional susceptibility to neuronal damage. In patients with Alzheimer’s disease, hippocampal and medial temporal lobe atrophy indicate early neuronal loss preferentially in key areas for learning and memory. We wanted to investigate whether this regional cortical thinning would be modulated by cardiovascular risk factors. We utilized high-resolution magnetic resonance imaging and a cortical unfolding technique to determine the cortical thickness of medial temporal subregions in 30 patients with Alzheimer’s disease. Cardiovascular risk was assessed using a sex-specific multivariable risk score. Greater cardiovascular risk was associated with cortical thinning in the hippocampus CA2/3/dentate gyrus area but not other hippocampal and medial temporal subregions. APOE genotype, a family history of Alzheimer’s disease, and age did not influence cortical thickness. Alzheimer’s disease-related atrophy could mask the influence of genetic risk factors or age on regional cortical thickness in medial temporal lobe regions, whereas the impact of vascular risk factors remains detectable. This highlights the importance of cardiovascular disease prevention and treatment in patients with Alzheimer’s disease.
Well-Posedness for Generalized Set Equilibrium Problems
Authors: Lin Yen-Cherng
Published: October 2013

We study the well-posedness for generalized set equilibrium problems (GSEP) and propose two types of the well-posed concepts for these problems in topological vector space settings. These kinds of well-posedness arise from some well-posedness in the vector settings. We also study the relationship between these well-posedness concepts and present several criteria for the well-posedness of GSEP. Our results are new or include as special cases recent existing results.
A Neural Network Model Can Explain Ventriloquism Aftereffect and Its Generalization across Sound Frequencies
Authors: Magosso Elisa , Cona Filippo , Ursino Mauro
Published: October 2013

Exposure to synchronous but spatially disparate auditory and visual stimuli produces a perceptual shift of sound location towards the visual stimulus (ventriloquism effect). After adaptation to a ventriloquism situation, enduring sound shift is observed in the absence of the visual stimulus (ventriloquism aftereffect). Experimental studies report opposing results as to aftereffect generalization across sound frequencies varying from aftereffect being confined to the frequency used during adaptation to aftereffect generalizing across some octaves. Here, we present an extension of a model of visual-auditory interaction we previously developed. The new model is able to simulate the ventriloquism effect and, via Hebbian learning rules, the ventriloquism aftereffect and can be used to investigate aftereffect generalization across frequencies. The model includes auditory neurons coding both for the spatial and spectral features of the auditory stimuli and mimicking properties of biological auditory neurons. The model suggests that different extent of aftereffect generalization across frequencies can be obtained by changing the intensity of the auditory stimulus that induces different amounts of activation in the auditory layer. The model provides a coherent theoretical framework to explain the apparently contradictory results found in the literature. Model mechanisms and hypotheses are discussed in relation to neurophysiological and psychophysical data.
Topical Nonsteroidal Anti-Inflammatory Drugs for Macular Edema
Authors: Russo Andrea , Costagliola Ciro , Delcassi Luisa , Parmeggiani Francesco , Romano Mario R. , dell'Omo Roberto , Semeraro Francesco
Published: October 2013

Nonsteroidal anti-inflammatory drugs (NSAIDs) are nowadays widely used in ophthalmology to reduce eye inflammation, pain, and cystoid macular edema associated with cataract surgery. Recently, new topical NSAIDs have been approved for topical ophthalmic use, allowing for greater drug penetration into the vitreous. Hence, new therapeutic effects can be achieved, such as reduction of exudation secondary to age-related macular degeneration or diabetic maculopathy. We provide an updated review on the clinical use of NSAIDs for retinal diseases, with a focus on the potential future applications.
Gender Differences in Fat Distribution and Inflammatory Markers among Arabs
Authors: Farooq Abdulaziz , Knez Wade L. , Knez Kelly , Al-Noaimi Asma , Grantham Justin , Mohamed-Ali Vidya
Published: October 2013

Recent studies from the Gulf region suggest that compared to men, women have a greater risk of developing metabolic syndrome (MeS).Objective. To investigate gender differences in body composition, adipokines, inflammatory markers, and aerobic fitness in a cohort of healthy Qatari adults.Participants. Healthy Qatari (n=58) were matched for age, gender, and body mass index.Methods. Body composition and regional fat distribution were determined by dual-energy X-ray absorptiometry and computerized tomography. Laboratory assessments included serum levels of fasting glucose, insulin, lipid profile analysis, adipokines, and inflammatory markers. Subjects were also evaluated for aerobic fitness.Results. Women had more adipose tissue in the total abdominal (P=0.04) and abdominal subcutaneous (P=0.07) regions compared to men. Waist circumference and indices of insulin sensitivity were similar; however, women had a more favourable lipid profile than men. Serum adiponectin and leptin levels were significantly higher in women, whereas inflammatory profiles were not different between men and women. Aerobic fitness was lower in women and was associated with abdominal fat accumulation.Conclusion. In premenopausal women, higher levels of adiponectin may support maintenance of insulin sensitivity and normolipidemia despite greater adiposity. However, poor aerobic fitness combined with abdominal fat accumulation may explain their greater future risk of MeS compared with men.
The Characterization of Lithium Titanate Microspheres Synthesized by a Hydrothermal Method
Authors: Liu Wei , Wang Yu , Jia Xiaolin , Xia Baojia
Published: October 2013

Lithium titanate microspheres were synthesized by a hydrothermal method. The structure and morphology of samples were characterized by X‐ray diffraction, infrared spectroscopy, Raman spectroscopy, scanning electron microscopy, and transmission electron microscopy, respectively. The specific surface area and average pore diameter of samples were studied by N2 adsorption‐desorption isotherms. The results indicated that amorphous phase changed to lithium titanium oxide hydrate, accompanying mesopores formed between agglomerated primary particles in hydrothermal reaction. After sintering, mesoporous Li4Ti5O12 microspheres assembled by nanosized particle were obtained and had a diameter of about 400–700 nm. Then, a possible formation process analogous to the Kirkendall effect was proposed. Moreover, the effect of sintering temperature on the electrochemical properties of Li4Ti5O12 microspheres was investigated.
Green Synthesis and In Vitro Biological Evaluation of Heteroaryl Chalcones and Pyrazolines of Medicinal Interest
Authors: Banewar Vishal
Published: October 2013

Pyrazolines are well known and important nitrogen containing 5‐membered heterocyclic compounds. In the present investigation, a series of various heteroaryl chalcones and pyrazolines were synthesized by condensing formylquinolines with diverse ketones. The newly synthesized 2‐pyrazolines were characterized on the basis of elemental analysis and spectroscopic data. All of the newly synthesized target compounds were selected by the NCI for in vitro biological evaluation. These active compounds exhibited broad spectrum of various biological activities. Most of the compounds showed potent activity.
Impact of Right-Sided Nephrectomy on Long-Term Outcomes in Retroperitoneoscopic Live Donor Nephrectomy at Single Center
Authors: Omoto Kazuya , Nozaki Taiji , Inui Masashi , Shimizu Tomokazu , Hirai Toshihito , Sawada Yugo , Ishida Hideki , Tanabe Kazunari
Published: October 2013

Objective.To assess the long-term graft survival of right-sided retroperitoneoscopic live donor nephrectomy (RPLDN), we compared the outcomes of right- and left-sided RPLDN.Methods.Five hundred and thirty-three patients underwent live donor renal transplantation with allografts procured by RPLDN from July 2001 to August 2010 at our institute. Of these, 24 (4.5%) cases were selected for right-sided RPLDN (R-RPLDN) according to our criteria for donor kidney selection. Study variables included peri- and postoperative clinical data.Results.No significant differences were found in the recipients' postoperative graft function and incidence of slow graft function. Despite significant increased warm ischemic time (WIT: mean 5.9 min versus 4.7 min, ) in R-RPLDN compared to that in L-RPLDN, there was no significant difference between the two groups regarding long-term patient and graft survival. The complication rate in R-RPLDN was not significantly different compared to that in L-RPLDN (17% versus 6.5%, ). No renal vein thrombosis was experienced in either groups.Conclusions.Although our study was retrospective and there was only a small number of R-RPLDN patients, R-RPLDN could be an option for laparoscopic live donor nephrectomy because of similar results, with the sole exception of WIT, in L-RPLDN, and its excellent long-term graft outcomes.
Improved Method for the Detection and Quantification ofNaegleria fowleriin Water and Sediment Using Immunomagnetic Separation and Real-Time PCR
Authors: Mull Bonnie J. , Narayanan Jothikumar , Hill Vincent R.
Published: October 2013

Primary amebic meningoencephalitis (PAM) is a rare and typically fatal infection caused by the thermophilic free-living ameba,Naegleria fowleri. In 2010, the first confirmed case of PAM acquired in Minnesota highlighted the need for improved detection and quantification methods in order to study the changing ecology ofN. fowleriand to evaluate potential risk factors for increased exposure. An immunomagnetic separation (IMS) procedure and real-time PCR TaqMan assay were developed to recover and quantifyN. fowleriin water and sediment samples. When one liter of lake water was seeded withN. fowleristrain CDC:V212, the method had an average recovery of 46% and detection limit of 14 amebas per liter of water. The method was then applied to sediment and water samples with unknownN. fowlericoncentrations, resulting in positive direct detections by real-time PCR in 3 out of 16 samples and confirmation ofN. fowlericulture in 6 of 16 samples. This study has resulted in a new method for detection and quantification ofN. fowleriin water and sediment that should be a useful tool to facilitate studies of the physical, chemical, and biological factors associated with the presence and dynamics ofN. fowleriin environmental systems.
Decreased Copper in Alzheimer’s Disease Brain Is Predominantly in the Soluble Extractable Fraction
Authors: Rembach Alan , Hare Dominic J. , Lind Monica , Fowler Christopher J. , Cherny Robert A. , McLean Catriona , Bush Ashley I. , Masters Colin L. , Roberts Blaine R.
Published: October 2013

Alzheimer’s disease (AD) is the leading cause of dementia and represents a significant burden on the global economy and society. The role of transition metals, in particular copper (Cu), in AD has become of significant interest due to the dyshomeostasis of these essential elements, which can impart profound effects on cell viability and neuronal function. We tested the hypothesis that there is a systemic perturbation in Cu compartmentalization in AD, within the brain as well as in the periphery, specifically within erythrocytes. Our results showed that the previously reported decrease in Cu within the human frontal cortex was confined to the soluble (P<0.05) and total homogenate (P<0.05) fractions. No differences were observed in Cu concentration in erythrocytes. Our data indicate that there is a brain specific alteration in Cu levels in AD localized to the soluble extracted material, which is not reflected in erythrocytes. Further studies using metalloproteomics approaches will be able to elucidate the metabolic mechanism(s) that results in the decreased brain Cu levels during the progression of AD.
An Approach of Laser-Induced Breakdown Spectroscopy to Detect Toxic Metals in Crushed Ice Ball
Authors: Agrawal Rahul , Pathak Ashok Kumar , Rai Awadhesh Kumar , Rai Gyanendra Kumar
Published: October 2013

This paper deals the application of laser-induced breakdown spectroscopy (LIBS) to toxic metals used as pigment in crushed ice-ball samples. The present work highlights the advantages of LIBS as in situ, real-time analytical tool for rapid detection of toxic or heavy metals like lead (Pb) and chromium (Cr) and non toxic elements like carbon (C), nitrogen (N), magnesium (Mg), calcium (Ca), sodium (Na), and potassium (K) in crushed ice-ball of different colors (red, green, yellow, pale yellow, and orange) collected from five different areas, with minimal sample preparation. For rapid surveillance of toxic metals we have used multivariate analysis, that is, principal component analysis (PCA) with the LIBS spectral data of ice-ball samples. This study suggests that LIBS coupled with PCA may be an instant diagnostic tool for identification and classification of adulterated and nonadulterated samples.
Herdsmen’s Adaptation to Climate Changes and Subsequent Impacts in the Ecologically Fragile Zone, China
Authors: Liu Yingcheng , Zhang Tao , Geng Xiaoli , He Liansheng , Pang Zhiguo
Published: October 2013

The change of land surface can exert significant influence on the future climate change. This study analyzed the effects of herdsmen’s adaptation to climate changes on the livestock breeding, income, and land surface dynamics with a land surface parameterization scheme. The empirical analysis was first carried out on the impacts of the adaptation measures of herdsmen on their income in the context of the climate change with the positive mathematical programming (PMP) model on the basis of the household survey data in the Three-River Source Region, an ecologically fragile area in Qinghai Province, China. Then, the land surface parameterization process is analyzed based on the agent-based model (ABM), which involves the herdsmen’s adaptation measures on climate change, and it also provides reference for the land surface change projection. The result shows that the climate change adaptation measures will have a positive effect on the increasing of the amount of herdsman’s livestock and income as well as future land surface dynamics. Some suggestions on the land use management were finally proposed, which can provide significant reference information for the land use planning.
Particle Acceleration by an Electromagnetic Wave
Authors: Dehnen Heinz
Published: October 2013

The relativistic equation of motion for an electrically charged massive point particle is integrated exactly for the case of a circularly polarized electromagnetic plane wave. The acceleration of the particle by the wave is calculated in detail, however, under neglection of the radiation damping. In spite of this simplification, the results are applied to a typical pulsar, where the maximum kinetic energy of accelerated protons reaches values of the order of the fastest cosmic ray particles.
Activation of the NFκB Pathway Enhances AhR Expression in Intestinal Caco-2 Cells
Authors: Champion S. , Sauzet C. , Bremond P. , Benbrahim K. , Abraldes J. , Seree E. , Barra Y. , Villard P. H.
Published: October 2013

Recent data suggest that apart from its well-known role in the regulation of xenobiotic metabolizing enzymes, AhR is also involved in inflammation. However, the influence of inflammation on AhR expression remains unknown. Here, we demonstrated that proinflammatory conditions induced by either PMA or IL-1β enhance AhR expression in Caco-2 cells. This was associated with an increase in AhR promoter activity. By means of directed mutagenesis experiments and the use of proteasome inhibitors, we demonstrated that inflammation-induced AhR expression involved the NFκB pathway but not AP-1. Moreover, conditioned media from PMA-treated Caco-2 cells were also able to induce AhR expression, and this induction was repressed by anti-IL-1β blocking antibodies. Similar results were obtained with conditioned media from PMA-treated THP-1 cells. Taken together, these data suggest that AhR could be involved in vivo in an inflammatory loop. AhR was recently suspected to be implicated in inflammatory bowel disease. Our results support this hypothesis and suggest that AhR could be a new target for inflammatory bowel disease patient management.
Expression of VEGF-A, Otx Homeobox and p53 Family Genes in Proliferative Vitreoretinopathy
Authors: Azzolini Claudio , Pagani Ilaria Stefania , Pirrone Cristina , Borroni Davide , Donati Simone , Al Oum Muna , Pigni Diana , Chiaravalli Anna Maria , Vinciguerra Riccardo , Simonelli Francesca , Porta Giovanni
Published: October 2013

Introduction. Proliferative vitreoretinopathy (PVR) is a severe inflammatory complication of retinal detachment. Pathological epiretinal membranes grow on the retina surface leading to contraction, and surgery fails in 5% to 10% of the cases. We evaluated the expression of VEGF-A, Otx1, Otx2, Otx3, and p53 family members from PVR specimens to correlate their role in inducing or preventing the pathology.Methods. Twelve retinal samples were taken from patients affected by PVR during therapeutic retinectomies in vitreoretinal surgery. Gene expression was evaluated using quantitative real-time reverse transcriptase PCR analysis and immunohistochemistry, using four healthy human retinae as control.Result. Controls showed basal expression of all genes. PVR samples showed little or no expression of Otx1 and variable expression of VEGF-A, Otx2, Otx3, p53, and p63 genes. Significant correlation was found among VEGF-A, Otx2, p53, and p63 and between Otx1 and Otx3.Conclusions. Otx homeobox, p53 family, and VEGF-A genes are expressed in PVR human retina. We individuated two possible pathways (VEGF-A, Otx2, p53, p63 and Otx1 and Otx3) involved in PVR progression that could influence in different manners the course of the pathology. Individuating the genetic pathways of PVR represents a novel approach to PVR therapies.
Formulation and Evaluation of Liquisolid Compacts for Olmesartan Medoxomil
Authors: Prajapati Shailesh T. , Bulchandani Hitesh H. , Patel Dashrath M. , Dumaniya Suresh K. , Patel Chhaganbhai N.
Published: October 2013

Olmesartan medoxomil is an angiotensin type II receptor blocker, antihypertensive agent, administered orally. It is highly lipophilic (log P 5.5) and a poorly water-soluble drug with absolute bioavailability of 26%. The poor dissolution rate of water-insoluble drugs is still a major problem confronting the pharmaceutical industry. The objective of the present investigation was to develop liquisolid compacts for olmesartan medoxomil to improve the dissolution rate. Liquisolid compacts were prepared using Acrysol El 135 as a solvent, Avicel PH 102, Fujicalin and Neusilin as carrier materials, and Aerosil as coating material in different ratios. The interaction between drug and excipients was characterized by DSC and FT-IR studies, which showed that there is no interaction between drug and excipients. The powder characteristics were evaluated by different flow parameters to comply with pharmacopoeial limits. The dissolution studies for liquisolid compacts and conventional formulations were carried out, and it was found that liquisolid compacts with 80% w/w of Acrysol EL 135 to the drug showed significant higher drug release rates than conventional tablets. Amongst carriers used Fujicalin and Neusilin were found to be more effective carrier materials for liquid adsorption.
Therapeutic Potential of Biologically Reduced Silver Nanoparticles from Actinomycete Cultures
Authors: Sukanya M. K. , Saju K. A. , Praseetha P. K. , Sakthivel G.
Published: October 2013

Silver nanoparticles are applied in nanomedicine from time immemorial and are still used as powerful antibiotic and anti-inflammatory agents. Antibiotics produced by actinomycetes are popular in almost all the therapeutic measures, and this study has proven that these microbes are also helpful in the biosynthesis of silver nanoparticles with good surface and size characteristics. Silver can be synthesized by various chemical methodologies, and most of them have turned to be toxic. This study has been successful in isolating the microbes from polluted environment, and subjecting them to the reduction of silver nanoparticles, characterizing the nanoparticles by UV spectrophotometry and transmission electron microscopy. The nanoparticles produced were tested for their antimicrobial property, and the zone of inhibition was greater than those produced by their chemically synthesized counterparts. Actinomycetes, helpful in bioremediating heavy metals, are useful for the production of metallic nanoparticles. The biosynthesized silver nanoparticles loaded with antibiotics prove to be better in killing the pathogens and have opened up new areas for developing nanobiotechnological research based on microbial applications.
A Dynamic Cooperative Scheme with Multiple Antennas for Indoor Mobile Robot Localization
Authors: Chang Chung-Liang , Wu Bo-Han
Published: October 2013

This paper proposes a spatial cooperative diversity and decision-making technique to enhance signal detection and indoor mobile robot positioning performance of a global positioning satellite system (GNSS) receiver. Though the adaptive antenna array technique in early research could effectively promote antijamming freedom, overcome time-varying system, and mitigate narrowband and wideband interferences, factors such as the decrease of signal magnitude caused by obstacles (especially in the indoor environment), multipath, and blanking effect caused by the change in antenna direction with the motion of mobile robot can degrade the detection and interference mitigation performance of GNSS receivers. This paper aims to develop a dynamic cooperative scheme to proceed with the switch, selection, combination, and optimization among antennas. In addition, a signal processing experimental platform is also established to receive actually indoor GNSS signals for verification. The proposed scheme is capable of effectively promoting the postcorrelation signal-to-noise ratio (SNR) capability of a GNSS receiver under the indoor environment.
The 3D Kuramoto-Sivashinsky Equation for Nonequilibrium Defects Interacting through Self-Consisting Strain and Nanostructuring of Solids
Authors: Emel’yanov V. I.
Published: October 2013

It is shown that the bulk defect-deformational (DD) nanostructuring of isotropic solids can be described by a closed three-dimensional (3D) nonlinear DD equation of the Kuramoto-Sivashinsry (KS) type for the nonequilibrium defect concentration, derived here in the framework of the nonlocal elasticity theory (NET). The solution to the linearized DDKS equation describes the threshold appearance of the periodic self-consistent strain modulation accompanied by the simultaneous formation of defect piles at extremes of the strain. The period and growth rate of DD nanostructure are determined. Based on the obtained results, a novel mechanism of nanostructuring of solids under the severe plastic deformation (SPD), stressing the role of defects generation and selforganization, described by the DDKS, is proposed. Theoretical dependencies of nanograin size on temperature and shear strain reproduce well corresponding critical dependencies obtained in experiments on nanostructuring of metals under the SPD, including the effect of saturation of nanofragmentation. The scaling parameter of the NET is estimated and shown to determine the limiting small grain size.
Some Intersections of the Weighted -Spaces
Authors: Abtahi F. , Amini H. G. , Lotfi H. A. , Rejali A.
Published: October 2013

Let be a locally compact group an arbitrary family of the weight functions on and . The locally convex space as a subspace of is defined. Also, some sufficient conditions for that space to be a Banach space are provided. Furthermore, for an arbitrary subset of and a positive submultiplicative weight function on , Banach subspace of is introduced. Then some algebraic properties of , as a Banach algebra under convolution product, are investigated.
Bilateral Low-Frequency Repetitive Transcranial Magnetic Stimulation of the Auditory Cortex in Tinnitus Patients Is Not Effective: A Randomised Controlled Trial
Authors: Hoekstra Carlijn E.L. , Versnel Huib , Neggers Sebastiaan F.W. , Niesten Marlien E.F. , van Zanten Gijsbert A.
Published: October 2013

Background: Although some therapies may be beneficial for some patients in reducing tinnitus, there is no curative therapy. Repetitive transcranial magnetic stimulation (rTMS) has been applied as a treatment for chronic tinnitus, but the effect remains controversial. Material and Methods: Fifty patients were treated with rTMS or placebo. Treatment consisted of 2,000 TMS pulses on each auditory cortex, at a rate of 1 Hz and an intensity of 110% of the individual motor threshold, on 5 consecutive days. rTMS and placebo effects were evaluated directly after treatment, after 1 week, and after 1, 3 and 6 months. Primary outcome was the Tinnitus Questionnaire (TQ). Secondary outcomes were the Tinnitus Handicap Inventory (THI) and a visual analogue scale. Results: At none of the follow-up evaluation moments a significant difference between rTMS and placebo was observed with respect to changes in TQ or THI scores relative to pretreatment scores. Multilevel modelling (MLM) analyses did not show a global treatment effect either. Patients with a higher degree of burden showed slightly greater improvement after rTMS (only significant on the THI with MLM analyses). Conclusion: Bilateral low-frequency rTMS of the auditory cortex was not effective in treating tinnitus.
Dyslipidemia, Coronary Artery Calcium, and Incident Atherosclerotic Cardiovascular Disease
Authors: Martin Seth S. , Blaha Michael J. , Blankstein Ron , Agatston Arthur , Rivera Juan J. , Virani Salim S. , Ouyang Pamela , Jones Steven R. , Blumenthal Roger S. , Budoff Matthew J. , Nasir Khurram
Published: October 2013

Background—

Worldwide clinical practice guidelines for dyslipidemia emphasize allocating statin therapy to those at the highest absolute atherosclerotic cardiovascular disease (CVD) risk.

Methods and Results—

We examined 5534 Multi-Ethnic Study of Atherosclerosis (MESA) participants who were not on baseline medications for dyslipidemia. Participants were classified by baseline coronary artery calcium (CAC) score (>0, ≥100) and the common clinical scheme of counting lipid abnormalities (LA), including low-density lipoprotein cholesterol ≥3.36 mmol/L (130 mg/dL), high-density lipoprotein cholesterol <1.03 mmol/L (40 mg/dL) for men or <1.29 mmol/L (50 mg/dL) for women, and triglycerides ≥1.69 mmol/L (150 mg/dL). Our main outcome measure was incident CVD (myocardial infarction, angina resulting in revascularization, resuscitated cardiac arrest, stroke, cardiovascular death). Over a median follow-up of 7.6 years, more than half of events (55%) occurred in the 21% of participants with CAC ≥100. Conversely, 65% of events occurred in participants with 0 or 1 LA. In those with CAC ≥100, CVD rates ranged from 22.7 to 29.5 per 1000 person-years across LA categories. In contrast, with CAC=0, CVD rates ranged from 2.7 to 5.9 per 1000 person-years across LA categories. Individuals with 0 LA and CAC ≥100 had a higher event rate compared with individuals with 3 LA but CAC=0 (22.7 versus 5.9 per 1000 person-years). Similar results were obtained when we classified LA using data set quartiles of total cholesterol/high-density lipoprotein cholesterol, low-density lipoprotein cholesterol, non–high-density lipoprotein cholesterol, or low-density lipoprotein particle concentration and guideline categories of low-density lipoprotein cholesterol or non–high-density lipoprotein cholesterol.

Conclusions—

CAC may have the potential to help match statin therapy to absolute CVD risk. Across the spectrum of dyslipidemia, event rates similar to secondary prevention populations were observed for patients with CAC ≥100.
Genetic Polymorphisms Regulating Dopamine Signaling in the Frontal Cortex Interact to Affect Target Detection under High Working Memory Load
Authors: Smith Christopher T. , Swift-Scanlan Theresa , Boettiger Charlotte A.
Published: October 2013

Frontal-dependent task performance is typically modulated by dopamine (DA) according to an inverted-U pattern, whereby intermediate levels of DA signaling optimizes performance. Numerous studies implicate trait differences in DA signaling based on differences in the catechol-O-methyltransferase (COMT) gene in executive function task performance. However, little work has investigated genetic variations in DA signaling downstream from COMT. One candidate is the DA- and cAMP-regulated phosphoprotein of molecular weight 32 kDa (DARPP-32), which mediates signaling through the D1-type DA receptor, the dominant DA receptor in the frontal cortex. Using an n-back task, we used signal detection theory to measure performance in a healthy adult population (n = 97) genotyped for single nucleotide polymorphisms in the COMT (rs4680) and DARPP-32 (rs907094) genes. Correct target detection (hits) and false alarms were used to calculate d′ measures for each working memory load (0-, 2-, and 3-back). At the highest load (3-back) only, we observed a significant COMT × DARPP-32 interaction, such that the DARPP-32 T/T genotype enhanced target detection in COMTValVal individuals, but impaired target detection in COMTMet carriers. These findings suggest that enhanced dopaminergic signaling via the DARPP-32 T allele aids target detection in individuals with presumed low frontal DA (COMTValVal) but impairs target detection in those with putatively higher frontal DA levels (COMTMet carriers). Moreover, these data support an inverted-U model with intermediate levels of DA signaling optimizing performance on tasks requiring maintenance of mental representations in working memory.