bluuebunny/crossref_metadata_2025 huggingface dataset:
Prevalence and Pathogenic Potential of Campylobacter Isolates from Free-Living, Human-Commensal American Crows
Authors: Weis Allison M. , Miller Woutrina A. , Byrne Barbara A. , Chouicha Nadira , Boyce Walter M. , Townsend Andrea K.
Published: December 2013

Recent studies have suggested a potential role for wild birds in zoonotic transmission ofCampylobacter jejuni, the leading cause of gastroenteritis in humans worldwide. In this study, we detectedCampylobacterspp. in 66.9% (85/127) of free-ranging American crows (Corvus brachyrhyncos) sampled in the Sacramento Valley of California in 2012 and 2013. Biochemical testing and sequence analysis of 16S rRNA revealed that 93% of isolates (n= 70) wereC. jejuni, with cytolethal distending toxin (CDT) and flagellin A genes detected by PCR in 20% and 46% of theC. jejuniisolates (n= 59), respectively. The high prevalence ofC. jejuni, coupled with the occurrence of known virulence markers CDT and flagellin A, demonstrates that crows shedCampylobacterspp. in their feces that are potentially pathogenic to humans. Crows are abundant in urban, suburban, and agricultural settings, and thus further study to determine their role in zoonotic transmission ofCampylobacterwill inform public health.
Multistrain Probiotic Modulation of Intestinal Epithelial Cells' Immune Response to a Double-Stranded RNA Ligand, Poly(I·C)
Authors: MacPherson Chad , Audy Julie , Mathieu Olivier , Tompkins Thomas A.
Published: December 2013

A commercially available product containing three probiotic bacterial strains (
Lactobacillus helveticus
R0052,
Bifidobacterium longum
subsp.
infantis
R0033, and
Bifidobacterium bifidum
R0071) was previously shown in animal trials to modulate both T
H
1 and T
H
2 immune responses. Clinical studies on this combination of bacteria have also shown positive health effects against seasonal winter diseases and rotavirus infection. The goal of this study was to use a well-established
in vitro
intestinal epithelial (HT-29) cell model that has been shown to constitutively express double-stranded RNA (dsRNA) sensors (Toll-like receptor 3 [TLR3], retinoic acid-inducible gene I, melanoma differentiation-associated gene 5, and dsRNA-activated protein kinase). By using the HT-29 cell model, we wanted to evaluate whether or not this combination of three bacteria had the capacity to immune modulate the host cell response to a dsRNA ligand, poly(I·C). Using a custom-designed, two-color expression microarray targeting genes of the human immune system, we investigated the response of HT-29 cells challenged with poly(I·C) both in the presence and in the absence of the three probiotic bacteria. We observed that the combination of the three bacteria had a major impact on attenuating the expression of genes connected to proinflammatory T
H
1 and antiviral innate immune responses compared to that obtained by the poly(I·C)-only challenge. Major pathways through which the multistrain combination may be eliciting its immune-modulatory effect include the TLR3 domain-containing adapter-inducing beta interferon (TRIF), mitogen-activated protein kinase, and NF-κB signaling pathways. Such a model may be useful for selecting potential biomarkers for the design of future clinical trials.
High-Yield, Zero-Leakage Expression System with a Translational Switch Using Site-Specific Unnatural Amino Acid Incorporation
Authors: Minaba Masaomi , Kato Yusuke
Published: December 2013

Synthetic biologists construct complex biological circuits by combinations of various genetic parts. Many genetic parts that are orthogonal to one another and are independent of existing cellular processes would be ideal for use in synthetic biology. However, our toolbox is still limited with respect to the bacterium
Escherichia coli
, which is important for both research and industrial use. The site-specific incorporation of unnatural amino acids is a technique that incorporates unnatural amino acids into proteins using a modified exogenous aminoacyl-tRNA synthetase/tRNA pair that is orthogonal to any native pairs in a host and is independent from other cellular functions. Focusing on the orthogonality and independency that are suitable for the genetic parts, we designed novel AND gate and translational switches using the unnatural amino acid 3-iodo-
l
-tyrosine incorporation system in
E. coli
. A translational switch was turned on after addition of 3-iodo-
l
-tyrosine in the culture medium within minutes and allowed tuning of switchability and translational efficiency. As an application, we also constructed a gene expression system that produced large amounts of proteins under induction conditions and exhibited zero-leakage expression under repression conditions. Similar translational switches are expected to be applicable also for eukaryotes such as yeasts, nematodes, insects, mammalian cells, and plants.
Molecular Characterization of a Novel
N
-Acetyltransferase from Chryseobacterium sp
Authors: Takenaka Shinji , Yoshida Kenji , Tanaka Kosei , Yoshida Ken-ichi
Published: December 2013

N
-Acetyltransferase from
Chryseobacterium
sp. strain 5-3B is an acetyl coenzyme A (acetyl-CoA)-dependent enzyme that catalyzes the enantioselective transfer of an acetyl group from acetyl-CoA to the amino group of
l
-2-phenylglycine to produce (2
S
)-2-acetylamino-2-phenylacetic acid. We purified the enzyme from strain 5-3B and deduced the N-terminal amino acid sequence. The gene, designated
natA
, was cloned with two other hypothetical protein genes; the three genes probably form a 2.5-kb operon. The deduced amino acid sequence of NatA showed high levels of identity to sequences of putative
N
-acetyltransferases of
Chryseobacterium
spp. but not to other known arylamine and arylalkylamine
N
-acetyltransferases. Phylogenetic analysis indicated that NatA forms a distinct lineage from known
N
-acetyltransferases. We heterologously expressed recombinant NatA (rNatA) in
Escherichia coli
and purified it. rNatA showed high activity for
l
-2-phenylglycine and its chloro- and hydroxyl-derivatives. The

K
m

and
V
max
values for
l
-2-phenylglycine were 0.145 ± 0.026 mM and 43.6 ± 2.39 μmol · min
−1
· mg protein
−1
, respectively. The enzyme showed low activity for 5-aminosalicylic acid and 5-hydroxytryptamine, which are reported as good substrates of a known arylamine
N
-acetyltransferase and an arylalkylamine
N
-acetyltransferase. rNatA had a comparatively broad acyl donor specificity, transferring acyl groups to
l
-2-phenylglycine and producing the corresponding 2-acetylamino-2-phenylacetic acids (relative activity with acetyl donors acetyl-CoA, propanoyl-CoA, butanoyl-CoA, pentanoyl-CoA, and hexanoyl-CoA, 100:108:122:10:<1).
Active Ammonia Oxidizers in an Acidic Soil Are Phylogenetically Closely Related to Neutrophilic Archaeon
Authors: Wang Baozhan , Zheng Yan , Huang Rong , Zhou Xue , Wang Dongmei , He Yuanqiu , Jia Zhongjun
Published: December 2013

All cultivated ammonia-oxidizing archaea (AOA) within the
Nitrososphaera
cluster (former soil group 1.1b) are neutrophilic. Molecular surveys also indicate the existence of
Nitrososphaera
-like phylotypes in acidic soil, but their ecological roles are poorly understood. In this study, we present molecular evidence for the chemolithoautotrophic growth of
Nitrososphaera
-like AOA in an acidic soil with pH 4.92 using DNA-based stable isotope probing (SIP). Soil microcosm incubations demonstrated that nitrification was stimulated by urea fertilization and accompanied by a significant increase in the abundance of AOA rather than ammonia-oxidizing bacteria (AOB). Real-time PCR analysis of
amoA
genes as a function of the buoyant density of the DNA gradient following the ultracentrifugation of the total DNA extracted from SIP microcosms indicated a substantial growth of soil AOA during nitrification. Pyrosequencing of the total 16S rRNA genes in the “heavy” DNA fractions suggested that archaeal communities were labeled to a much greater extent than soil AOB. Acetylene inhibition further showed that
13
CO
2
assimilation by nitrifying communities depended solely on ammonia oxidation activity, suggesting a chemolithoautotrophic lifestyle. Phylogenetic analysis of both
13
C-labeled
amoA
and 16S rRNA genes revealed that most of the active AOA were phylogenetically closely related to the neutrophilic strains
Nitrososphaera viennensis
EN76 and JG1 within the
Nitrososphaera
cluster. Our results provide strong evidence for the adaptive growth of
Nitrososphaera
-like AOA in acidic soil, suggesting a greater metabolic versatility of soil AOA than previously appreciated.
Identification and Upregulation of Biosynthetic Genes Required for Accumulation of Mycosporine-2-Glycine under Salt Stress Conditions in the Halotolerant Cyanobacterium Aphanothece halophytica
Authors: Waditee-Sirisattha Rungaroon , Kageyama Hakuto , Sopun Warangkana , Tanaka Yoshito , Takabe Teruhiro
Published: December 2013

Mycosporine-like amino acids (MAAs) are valuable molecules that are the basis for important photoprotective constituents. Here we report molecular analysis of mycosporine-like amino acid biosynthetic genes from the halotolerant cyanobacterium
Aphanothece halophytica
, which can survive at high salinity and alkaline pH. This extremophile was found to have a unique MAA core (4-deoxygadusol)-synthesizing gene separated from three other genes.
In vivo
analysis showed accumulation of the mycosporine-2-glycine but not shinorine or mycosporine-glycine. Mycosporine-2-glycine accumulation was stimulated more under the stress condition of high salinity than UV-B radiation. The
Aphanothece
MAA biosynthetic genes also manifested a strong transcript level response to salt stress. Furthermore, the transformed
Escherichia coli
and
Synechococcus
strains expressing four putative
Aphanothece
MAA genes under the control of a native promoter were found to be capable of synthesizing mycosporine-2-glycine. The accumulation level of mycosporine-2-glycine was again higher under the high-salinity condition. In the transformed
E. coli
cells, its level was approximately 85.2 ± 0.7 μmol/g (dry weight). Successful production of a large amount of mycosporine in these cells provides a new opportunity in the search for an alternative natural sunscreen compound source.
Accumulation of Polyphosphate in Lactobacillus spp. and Its Involvement in Stress Resistance
Authors: Alcántara Cristina , Blasco Amalia , Zúñiga Manuel , Monedero Vicente
Published: December 2013

Polyphosphate (poly-P) is a polymer of phosphate residues synthesized and in some cases accumulated by microorganisms, where it plays crucial physiological roles such as the participation in the response to nutritional stringencies and environmental stresses. Poly-P metabolism has received little attention in
Lactobacillus
, a genus of lactic acid bacteria of relevance for food production and health of humans and animals. We show that among 34 strains of
Lactobacillus
, 18 of them accumulated intracellular poly-P granules, as revealed by specific staining and electron microscopy. Poly-P accumulation was generally dependent on the presence of elevated phosphate concentrations in the culture medium, and it correlated with the presence of polyphosphate kinase (
ppk
) genes in the genomes. The
ppk
gene from
Lactobacillus
displayed a genetic arrangement in which it was flanked by two genes encoding exopolyphosphatases of the Ppx-GppA family. The
ppk
functionality was corroborated by its disruption (LCABL_27820 gene) in
Lactobacillus casei
BL23 strain. The constructed
ppk
mutant showed a lack of intracellular poly-P granules and a drastic reduction in poly-P synthesis. Resistance to several stresses was tested in the
ppk
-disrupted strain, showing that it presented a diminished growth under high-salt or low-pH conditions and an increased sensitivity to oxidative stress. These results show that poly-P accumulation is a characteristic of some strains of lactobacilli and may thus play important roles in the physiology of these microorganisms.
FigA, a Putative Homolog of Low-Affinity Calcium System Member Fig1 in Saccharomyces cerevisiae, Is Involved in Growth and Asexual and Sexual Development in Aspergillus nidulans
Authors: Zhang Shizhu , Zheng Hailin , Long Nanbiao , Carbó Natalia , Chen Peiying , Aguilar Pablo S. , Lu Ling
Published: December 2013

Calcium-mediated signaling pathways are widely employed in eukaryotes and are implicated in the regulation of diverse biological processes. In
Saccharomyces cerevisiae
, at least two different calcium uptake systems have been identified: the high-affinity calcium influx system (HACS) and the low-affinity calcium influx system (LACS). Compared to the HACS, the LACS in fungi is not well known. In this study, FigA, a homolog of the LACS member Fig1 from
S. cerevisiae
, was functionally characterized in the filamentous fungus
Aspergillus nidulans
. Loss of
figA
resulted in retardant hyphal growth and a sharp reduction of conidial production. Most importantly, FigA is essential for the homothallic mating (self-fertilization) process; further, FigA is required for heterothallic mating (outcrossing) in the absence of HACS
midA
. Interestingly, in a
figA
deletion mutant, adding extracellular Ca
2+
rescued the hyphal growth defects but could not restore asexual and sexual reproduction. Furthermore, quantitative PCR results revealed that
figA
deletion sharply decreased the expression of
brlA
and
nsdD
, which are known as key regulators during asexual and sexual development, respectively. In addition, green fluorescent protein (GFP) tagging at the C terminus of FigA (FigA::GFP) showed that FigA localized to the center of the septum in mature hyphal cells, to the location between vesicles and metulae, and between the junctions of metulae and phialides in conidiophores. Thus, our findings suggest that FigA, apart from being a member of a calcium uptake system in
A. nidulans
, may play multiple unexplored roles during hyphal growth and asexual and sexual development.
Solanesyl Diphosphate Synthase, an Enzyme of the Ubiquinone Synthetic Pathway, Is Required throughout the Life Cycle of Trypanosoma brucei
Authors: Lai De-Hua , Poropat Estefanía , Pravia Carlos , Landoni Malena , Couto Alicia S. , Pérez Rojo Fernando G. , Fuchs Alicia G. , Dubin Marta , Elingold Igal , Rodríguez Juan B. , Ferella Marcela , Esteva Mónica I. , Bontempi Esteban J. , Lukeš Julius
Published: December 2013

Ubiquinone 9 (UQ9), the expected product of the long-chain solanesyl diphosphate synthase of
Trypanosoma brucei
(TbSPPS), has a central role in reoxidation of reducing equivalents in the mitochondrion of
T. brucei
. The ablation of TbSPPS gene expression by RNA interference increased the generation of reactive oxygen species and reduced cell growth and oxygen consumption. The addition of glycerol to the culture medium exacerbated the phenotype by blocking its endogenous generation and excretion. The participation of TbSPPS in UQ synthesis was further confirmed by growth rescue using UQ with 10 isoprenyl subunits (UQ10). Furthermore, the survival of infected mice was prolonged upon the downregulation of TbSPPS and/or the addition of glycerol to drinking water. TbSPPS is inhibited by 1-[(
n
-oct-1-ylamino)ethyl] 1,1-bisphosphonic acid, and treatment with this compound was lethal for the cells. The findings that both UQ9 and ATP pools were severely depleted by the drug and that exogenous UQ10 was able to fully rescue growth of the inhibited parasites strongly suggest that TbSPPS and UQ synthesis are the main targets of the drug. These two strategies highlight the importance of TbSPPS for
T. brucei
, justifying further efforts to validate it as a new drug target.
A preliminary evaluation of the effects of opioids on innate and adaptive human in vitro immune function
Authors: Boland Jason W , Foulds Gemma A , Ahmedzai Sam H , Pockley A Graham
Published: December 2013

Background

Studies have demonstrated that whereas some opioids have little effect on immunity (eg, buprenorphine), others can be immunosuppressive (eg, morphine) or immunostimulatory (eg, tramadol). However, a variety of approaches have been used, especially in vitro and animal models, and the findings are variable. We hypothesised that opioids have differential effects on immunity via direct actions on neutrophils, monocytes, natural killer (NK) and T cells, and this is the first study to systematically evaluate the influence of eight opioids on neutrophil and monocyte phagocytosis and oxidative burst responses, NK cell cytotoxicity and T cell responsiveness in vitro.

Methods

Peripheral blood was obtained from healthy volunteers, and the effects of clinically relevant concentrations of morphine, tramadol, fentanyl, buprenorphine, methadone, oxycodone, diamorphine and codeine on phagocytosis and oxidative burst responses were determined using whole blood flow cytometry. The influence of opioids on the capacity of resting and IL-2 stimulated isolated peripheral blood mononuclear cells (PBMCs) to kill NK cell-sensitive K562 cells, and the responsiveness of PBMC subpopulations to IL-2 and polyclonal stimulation were also evaluated.

Results

Methadone, oxycodone and diamorphine inhibited the production of IL-6 by IL-2 stimulated PBMCs. None of the opioids consistently influenced the other measured immune parameters, although there was a trend for morphine, tramadol, fentanyl and buprenorphine to inhibit phagocytosis and oxidative burst responses toEscherichia coli.

Conclusions

Preliminary studies using standardised in vitro methodologies have demonstrated that some therapeutic opioids suppress IL-6 production. Although this might potentially suppress bacterial defence mechanisms, it would have little direct effect on anticancer immunity. These findings should be confirmed in larger in vitro and clinical studies.
REDUCING THE BULK IN THE BULK SYNCHRONOUS PARALLEL MODEL
Authors: BARRETT R. F. , VAUGHAN C. T. , HAMMOND S. D. , ROWETH D.
Published: December 2013

For over two decades the dominant means for enabling portable performance of computational science and engineering applications on parallel processing architectures has been the bulk-synchronous parallel programming (BSP) model. Code developers, motivated by performance considerations to minimize the number of messages transmitted, have typically pursued a strategy of aggregating message data into fewer, larger messages. Emerging and future high-performance architectures, especially those seen as targeting Exascale capabilities, provide motivation and capabilities for revisiting this approach. In this paper we explore alternative configurations within the context of a large-scale complex multi-physics application and a proxy that represents its behavior, presenting results that demonstrate some important advantages as the number of processors increases in scale.
LEARNING UNDER CONCEPT DRIFT USING A NEURO-EVOLUTIONARY ENSEMBLE
Authors: ESCOVEDO TATIANA , DA CRUZ ANDRÉ V. ABS , VELLASCO MARLEY M. B. R. , KOSHIYAMA ADRIANO S.
Published: December 2013

This work describes the use of a weighted ensemble of neural network classifiers for adaptive learning. We train the neural networks by means of a quantum-inspired evolutionary algorithm (QIEA). The QIEA is also used to determine the best weights for each classifier belonging to the ensemble when a new block of data arrives. After running several simulations using two different datasets and performing two different analysis of the results, we show that the proposed algorithm, named neuro-evolutionary ensemble (NEVE), was able to learn the data set and to quickly respond to any drifts on the underlying data, indicating that our model can be a good alternative to address concept drift problems. We also compare the results obtained by our model with an existing algorithm, Learn++.NSE, in two different nonstationary scenarios.
SVM AND NN BASED OFFLINE SIGNATURE VERIFICATION
Authors: PAL SRIKANTA , ALAEI ALIREZA , PAL UMAPADA , BLUMENSTEIN MICHAEL
Published: December 2013

Among all of the biometric authentication systems, handwritten signatures are considered as the most legally and socially accepted attributes for personal verification. The objective of this paper is to present an empirical contribution toward the understanding of a threshold-based signature verification technique involving off-line Bangla (Bengali) signatures. Experiments on signature verification concerning non-English signatures are an important consideration in the signature verification area. Only very few research works employing signatures of Indian script have been considered in the field of non-English based signature verification. To fill this gap, a threshold-based scheme for the verification of off-line Bangla signatures is proposed. Some techniques such as under-sampled bitmap, intersection/end point and directional chain code are employed for feature extraction. The thresholds are computed based on the similarity measures obtained employing the nearest neighbor classifier. The SVM classifier has also been considered for mainly comparative experimental result generation. Furthermore, a Bangla signature database, which consists of 2400 (100 × 24) genuine signatures and 3000 (100 × 30) forgeries, has been created and is employed for experimentation. An average error rate (AER) of 12.33% was obtained as the best verification result using directional chain code features in this research work. As a comparative study, a different dataset (GPDS-160) has also been considered.
The absence of insulin signaling in the heart induces changes in potassium channel expression and ventricular repolarization
Authors: Lopez-Izquierdo Angelica , Pereira Renata O. , Wende Adam R. , Punske Bonnie B. , Abel E. Dale , Tristani-Firouzi Martin
Published: December 2013

Diabetes mellitus increases the risk for cardiac dysfunction, heart failure, and sudden death. The wide array of neurohumoral changes associated with diabetes pose a challenge to understanding the roles of specific pathways that alter cardiac function. Here, we use a mouse model with cardiomyocyte-restricted deletion of insulin receptors (CIRKO, cardiac-specific insulin receptor knockout) to study the specific effects of impaired cardiac insulin signaling on ventricular repolarization, independent of the generalized metabolic derangements associated with diabetes. Impaired insulin action caused a reduction in mRNA and protein expression of several key K+ channels that dominate ventricular repolarization. Specifically, components of transient outward K+ current fast component ( Ito,fast; Kv4.2 and KChiP2) were reduced, consistent with a reduction in the amplitude of Ito,fast in isolated left ventricular CIRKO myocytes, compared with littermate controls. The reduction in Ito,fast resulted in ventricular action potential prolongation and prolongation of the QT interval on the surface ECG. These results support the notion that the lack of insulin signaling in the heart is sufficient to cause the repolarization abnormalities described in other animal models of diabetes.
The p66Shc adapter protein regulates the morphogenesis and epithelial maturation of fetal mouse lungs
Authors: Lee M. K. , Smith S. M. , Banerjee Maalika M. , Li Changgong , Minoo Parviz , Volpe M. V. , Nielsen H. C.
Published: December 2013

Many signaling pathways are mediated by Shc adapter proteins that, in turn, are expressed as three isoforms with distinct functions. The p66Shc isoform antagonizes proliferation, regulates oxidative stress, and mediates apoptosis. It is highly expressed in the canalicular but not the later stages of mouse lung development, and its expression persists in bronchopulmonary dysplasia, a chronic disease associated with premature birth. These observations suggest that p66Shc has a developmental function. However, constitutive p66Shc deletion yields no morphological phenotype, and the structure of the Shc gene precludes its inducible deletion. To elucidate its function in lung development, we transfected p66Shc or nonsilencing small-interfering RNA (siRNA) into the epithelia of embryonic day 11 mouse lungs that were then cultured for 3 days and analyzed morphometrically. To assess cellular proliferation and epithelial differentiation, lung explants were immunostained and immunoblotted for p66Shc, proliferating cell nuclear antigen (PCNA), the proximal airway differentiation antigens Clara cell 10-kDa protein (CC10) and thyroid transcription factor (TTF)-1, and the alveolar surfactant proteins (SP)-A, -B, and -C. Explants transfected with nonsilencing siRNA demonstrated specific epithelial uptake and normal morphological development relative to uninjected controls. In contrast, transfection with p66Shc siRNA significantly increased lumenal cross-sectional areas, decreased branching, and increased epithelial proliferation ( P < 0.05 for all). Relative to controls, the expression of SP-B, SP-C, CC10, and TTF-1 was decreased by p66Shc knockdown. SP-A was not expressed in either control or treated lungs. These data suggest that p66Shc attenuates epithelial proliferation while promoting both distal and proximal epithelial maturation.
Functional assessment of hyperoxia-induced lung injury after preterm birth in the rabbit
Authors: Richter Jute , Toelen Jaan , Vanoirbeek Jeroen , Kakigano Aiko , DeKoninck Philip , Verbeken Eric , Deprest Jan
Published: December 2013

The objective of this study was to document early neonatal (7 days) pulmonary outcome in the rabbit model for preterm birth and hyperoxia-induced lung injury. Preterm pups were delivered at 28 days (term = 31 days; early saccular phase of lung development) by cesarean section, housed in an incubator, and gavage fed for 7 days. Pups were divided into the following groups: 1) normoxia (21% O2; normoxia group) and 2) and hyperoxia (>95% O2; hyperoxia group). Controls were pups born at term who were housed in normoxic conditions (control group). Outcome measures were survival, pulmonary function tests using the whole body plethysmograph and forced oscillation technique, and lung morphometry. There was a significant difference in survival of preterm pups whether they were exposed to normoxia (83.3%) or hyperoxia (55.9%). Hyperoxic exposure was associated with increased tissue damping and elasticity and decreased static compliance compared with normoxic controls ( P < 0.01). Morphometry revealed an increased linear intercept and increased mean wall transection length, which translates to larger alveoli with septal thickening in hyperoxia compared with normoxia ( P < 0.01). In conclusion, the current experimental hyperoxic conditions to which preterm pups are exposed induce the typical clinical features of bronchopulmonary dysplasia. This model will be used to study novel preventive or therapeutic interventions.
Transglutaminase 2-mediated serotonylation in pulmonary hypertension
Authors: Penumatsa K. C. , Fanburg B. L.
Published: December 2013

The monoamine serotonin (5-HT) has been previously implicated in pulmonary arterial remodeling and is considered a potential therapeutic target for the disease pulmonary arterial hypertension (PAH). More recently, it has been recognized that the enzyme tissue transglutaminase (TG2) mediates cross-linking of proteins with 5-HT, a posttranslational process of monoaminylation known as “serotonylation.” TG2 activity and serotonylation of protein participate in both smooth muscle proliferation and contraction produced by 5-HT. Indeed, markedly increased TG2 activity has now been identified in lung tissue of an experimental rodent model of pulmonary hypertension, and elevated serotonylation of fibronectin and the signaling molecule Rho, downstream products of transglutamidation, have been found in blood of patients with PAH. The basic mechanism by which TG2 is activated and the potential role(s) of serotonylated proteins in pulmonary hypertension remain a mystery. In the present review we have tried to address the current understanding of 5-HT metabolism in pulmonary hypertension and relate it to what is currently known about the evolving cellular process of serotonylation.
Caffeine accelerates recovery from general anesthesia
Authors: Wang Qiang , Fong Robert , Mason Peggy , Fox Aaron P. , Xie Zheng
Published: December 2013

General anesthetics inhibit neurotransmitter release from both neurons and secretory cells. If inhibition of neurotransmitter release is part of an anesthetic mechanism of action, then drugs that facilitate neurotransmitter release may aid in reversing general anesthesia. Drugs that elevate intracellular cAMP levels are known to facilitate neurotransmitter release. Three cAMP elevating drugs (forskolin, theophylline, and caffeine) were tested; all three drugs reversed the inhibition of neurotransmitter release produced by isoflurane in PC12 cells in vitro. The drugs were tested in isoflurane-anesthetized rats. Animals were injected with either saline or saline containing drug. All three drugs dramatically accelerated recovery from isoflurane anesthesia, but caffeine was most effective. None of the drugs, at the concentrations tested, had significant effects on breathing rates, O2saturation, heart rate, or blood pressure in anesthetized animals. Caffeine alone was tested on propofol-anesthetized rats where it dramatically accelerated recovery from anesthesia. The ability of caffeine to accelerate recovery from anesthesia for different chemical classes of anesthetics, isoflurane and propofol, opens the possibility that it will do so for all commonly used general anesthetics, although additional studies will be required to determine whether this is in fact the case. Because anesthesia in rodents is thought to be similar to that in humans, these results suggest that caffeine might allow for rapid and uniform emergence from general anesthesia in human patients.
Influence of Electric Field Coupling Model on the Simulated Performances of a GaN Based Planar Nanodevice
Authors: Xu K. Y. , Wang Z. N. , Wang Y. N. , Xiong J. W. , Wang G.
Published: December 2013

The performances of a two‐dimensional electron gas (2DEG) based planar nanodevice are studied by a two‐dimensional‐three‐dimensional (2D‐3D) combined model and an entirely 2D model. In both models, 2DEGs are depicted by 2D ensemble Monte Carlo (EMC) method. However electric field distributions in the devices are obtained by self‐consistently solving 2D and 3D Poisson equations for the 2D model and the 2D‐3D model, respectively. Simulation results obtained by both models are almost the same at low bias while showing distinguished differences at high bias. The 2D model predicts larger output current and slightly higher threshold voltage of Gunn oscillations. Although the fundamental frequencies of current oscillations obtained by both models are similar, the deviation of wave shape from sinusoidal waveform obtained by the 2D model is more serious than that obtained by 2D‐3D model. Moreover, results obtained by the 2D model are more sensitive both to the bias conditions and to the change of device parameters. Interestingly, a look‐like second harmonic oscillation has been observed at DC bias. We contribute the origin of divergences in simulation results to the different coupling path of electric field in the two models. And the second‐harmonic oscillations at DC bias should be the result of the appearance of concomitant oscillations beside the channel excited by strong electric‐field effects.
Regularity in terms of Hyperideals
Authors: Hila Kostaq , Davvaz Bijan , Naka Krisanthi , Dine Jani
Published: December 2013

This paper deals with the algebraic hypersystems. The notion of regularity of different type of algebraic systems has been introduced and characterized by different authors such as Iseki, Kovacs, and Lajos. We generalize this notion to algebraic hypersystems giving a unified generalization of the characterizations of Kovacs, Iseki, and Lajos. We generalize also the concept of ideal introducing the notion of j-hyperideal and hyperideal of an algebraic hypersystem. It turns out that the description of regularity in terms of hyperideals is intrinsic to associative hyperoperations in general. The main theorem generalizes to algebraic hypersystems some results on regular semigroups and regular rings and expresses a necessary and sufficient condition by means of principal hyperideals. Furthermore, two more theorems are obtained: one is concerned with
a necessary and sufficient condition for an associative, commutative algebraic hypersystem to be regular and the other is concerned with nilpotent elements in the algebraic hypersystem.
Error Analysis of Some Demand Simplifications in Hydraulic Models of Water Supply Networks
Authors: Izquierdo Joaquín , Campbell Enrique , Montalvo Idel , Pérez-García Rafael , Ayala-Cabrera David
Published: December 2013

Mathematical modeling of water distribution networks makes use of simplifications aimed to optimize the development and use of the mathematical models involved. Simplified models are used systematically by water utilities, frequently with no awareness of the implications of the assumptions used. Some simplifications are derived from the various levels of granularity at which a network can be considered. This is the case of some demand simplifications, specifically, when consumptions associated with a line are equally allocated to the ends of the line. In this paper, we present examples of situations where this kind of simplification produces models that are very unrealistic. We also identify the main variables responsible for the errors. By performing some error analysis, we assess to what extent such a simplification is valid. Using this information, guidelines are provided that enable the user to establish if a given simplification is acceptable or, on the contrary, supplies information that differs substantially from reality. We also develop easy to implement formulae that enable the allocation of inner line demand to the line ends with minimal error; finally, we assess the errors associated with the simplification and locate the points of a line where maximum discrepancies occur.
Improved Magnetotelluric Zohdy-Oldenburg Direct Inversion
Authors: Cao Hui , Liu Yun , Wang Kun Peng
Published: December 2013

Based on researches of Baiyao (1995) and Zhang and Xu (2001), this paper proposes an improved 2D MT Zohdy-Oldenburg direct inversion method, in the least-square sense, embodying the features of Zohdy’s ratio method and Oldenburg’s difference method, in the condition of rugged topography, with phase information. It bypasses large calculations of the Jacobian matrix and large sparse linear systems of equations and enables direct modifications and comparisons of the model parameters. According to the calculation and analysis of examples, it shows faster convergence and higher precision. In contrast with the conventional linear inversion, the calculation speed of this new method can be increased by more than 10 times.
Plasma Fatty Acid Binding Protein 4 and Risk of Sudden Cardiac Death in Older Adults
Authors: Djoussé Luc , Maziarz Marlena , Biggs Mary L. , Ix Joachim H. , Zieman Susan J. , Kizer Jorge R. , Lemaitre Rozenn N. , Mozaffarian Dariush , Tracy Russell P. , Mukamal Kenneth J. , Siscovick David S. , Sotoodehnia Nona
Published: December 2013

Although fatty acid binding protein 4 (FABP4) may increase risk of diabetes and exert negative cardiac inotropy, it is unknown whether plasma concentrations of FABP4 are associated with incidence of sudden cardiac death (SCD). We prospectively analyzed data on 4,560 participants of the Cardiovascular Health Study. FABP4 was measured at baseline using ELISA, and SCD events were adjudicated through review of medical records. We used Cox proportional hazards to estimate effect measures. During a median followup of 11.8 years, 146 SCD cases occurred. In a multivariable model adjusting for demographic, lifestyle, and metabolic factors, relative risk of SCD associated with each higher standard deviation (SD) of plasma FABP4 was 1.15 (95% CI: 0.95–1.38),P=0.15. In a secondary analysis stratified by prevalent diabetes status, FABP4 was associated with higher risk of SCD in nondiabetic participants, (RR per SD higher FABP4: 1.33 (95% CI: 1.07–1.65),P=0.009) but not in diabetic participants (RR per SD higher FABP4: 0.88 (95% CI: 0.62–1.27),P=0.50),Pfor diabetes-FABP4 interaction 0.049. In summary, a single measure of plasma FABP4 obtained later in life was not associated with the risk of SCD in older adults overall. Confirmation of our post-hoc results in nondiabetic people in other studies is warranted.
New Medium for Pharmaceutical Grade Arthrospira
Authors: Amara Amro A. , Steinbüchel Alexander
Published: December 2013

The aim of this study is to produce a pharmaceutical grade single cell product of Arthrospira from a mixed culture. We have designed a medium derived from a combination between George’s and Zarrouk’s media. Our new medium has the ability to inhibit different forms of cyanobacterium and microalgae except the Chlorella. The medium and the cultivation conditions have been investigated to map the points where only Arthrospira could survive. For that, a mixed culture of pure Chlorella and Arthrospira (~90 : 10) has been used to develop the best medium composition that can lead to the enrichment of the Arthrospira growth and the inhibition of the Chlorella growth. To enable better control and to study its growth, an 80 l photobioreactor has been used. We have used high saline (2xA-St) medium which has been followed by in fermentor reducing its concentration to 1.5x. The investigation proves that Chlorella has completely disappeared. A method and a new saline medium have been established using a photobioreactor for in fermentor production of single cell Arthrospira. Such method enables the production of pure pharmaceutical grade Arthrospira for medicinal and pharmaceutical applications or as a single cell protein.
Estimation of Peak Flood Discharge for an Ungauged River: A Case Study of the Kunur River, West Bengal
Authors: Roy Suvendu , Mistri Biswaranjan
Published: December 2013

Due to unavailability of sufficient discharge data for many rivers, hydrologists have used indirect methods for deriving flood discharge amount, that is, application of channel geometry and hydrological models, for the estimation of peak discharge in the selected ungauged river basin(s) in their research/project works. This paper has studied the estimation of peak flood discharge of the Kunur River Basin, a major tributary of the Ajay River in the lower Gangetic plain. To achieve this objective, field measurements, GIS technique, and several channel geometry equations are adopted. Three important geomorphic based hydrological models—manning’s equation, kinematic wave parameter (KWP), and SCS curve number (CN) method—have been used for computing peak discharge during the flood season, based on daily rainfall data of September, 2000. Peak discharges, calculated by different given models, are 239.44 m3/s, 204.08 m3/s, and 146.52 m3/s, respectively. The hydrograph has demonstrated the sudden increase with heavy rainfall from the 18th to the 22nd of September, 2000. As a result, a havoc flood condition was generated in the confluence zone of Ajay and Kunur Rivers. This hydrograph might be not only successful application for flood forecasting but also for management of the lower Ajay River Basin as well as the downstream area of Kunur Basin.
Spatiotemporal Variation and Risk Assessment of Pesticides in Water of the Lower Catchment Basin of Acheloos River, Western Greece
Authors: Stamatis Nikolaos , Hela Dimitra , Triantafyllidis Vassilios , Konstantinou Ioannis
Published: December 2013

A three‐year monitoring survey (March 2005–February 2008) was conducted to investigate, on monthly basis, the presence of thirty pesticides belonging to various categories and metabolites, in Acheloos River (Western Greece), one of the most important water resources in Greece. Six sampling stations along the river were established. Water analyses were performed using solid‐phase extraction combined with gas chromatography with flame thermionic detector and mass spectrometry. Statistical analysis using one‐way ANOVA and Duncan’s multiple range test (P < 0.05) was used to compare annual mean concentrations of pesticides, seasonal and spatial distribution. In general, the highest mean concentrations of the pesticides were recorded at the three stations downstream. The greatest average concentrations were determined during spring and summer in agreement with the pesticide application period. The observed lower concentrations after 2006 reflect the land‐use change because of the elimination of tobacco, the main cultivation of the area for many decades. The compounds most frequently detected were diazinon (78.6%), DEA (69.3%), and fenthion (52.6%). Environmental risk assessment using risk quotient (RQ) approach showed high risk for six insecticides in 2005 and one in 2007. A compliance with the European Environmental Quality Standards (EQS) was observed for the priority pesticides.
Molecular Modeling of Lectin-Like Protein fromAcacia farnesianaReveals a Possible Anti-Inflammatory Mechanism in Carrageenan-Induced Inflammation
Authors: Abrantes Vanessa Erika Ferreira , Matias da Rocha Bruno Anderson , Batista da Nóbrega Raphael , Silva-Filho José Caetano , Teixeira Claudener Souza , Cavada Benildo Sousa , Gadelha Carlos Alberto de Almeida , Ferreira Sergio Henrique , Figueiredo Jozi Godoy , Santi-Gadelha Tatiane , Delatorre Plinio
Published: December 2013

Acacia farnesianalectin-like protein (AFAL) is a chitin-binding protein and has been classified as phytohaemagglutinin fromPhaseolus vulgaris(PHA). Legume lectins are examples for structural studies, and this family of proteins shows a remarkable conservation in primary, secondary, and tertiary structures. Lectins have ability to reduce the effects of inflammation caused by phlogistic agents, such as carrageenan (CGN). This paper explains the anti-inflammatory activity of AFAL through structural comparison with anti-inflammatory legume lectins. The AFAL model was obtained by molecular modeling and molecular docking with glycan and carrageenan were performed to explain the AFAL structural behavior and biological activity.Pisum sativumlectin was the best template for molecular modeling. The AFAL structure model is folded as aβsandwich. The model differs from template in loop regions, number ofβstrands and carbohydrate-binding site. Carrageenan and glycan bind to different sites on AFAL. The ability of AFAL binding to carrageenan can be explained by absence of the sixthβ-strand (posteriorβsheets) and twoβstrands in frontal region. AFAL can inhibit pathway inflammatory process by carrageenan injection by connecting to it and preventing its entry into the cell and triggers the reaction.
Prediction of IL4 Inducing Peptides
Authors: Dhanda Sandeep Kumar , Gupta Sudheer , Vir Pooja , Raghava G. P. S.
Published: December 2013

The secretion of Interleukin-4 (IL4) is the characteristic of T-helper 2 responses. IL4 is a cytokine produced by CD4+ T cells in response to helminthes and other extracellular parasites. It has a critical role in guiding antibody class switching, hematopoiesis and inflammation, and the development of appropriate effector T-cell responses. In this study, it is the first time an attempt has been made to understand whether it is possible to predict IL4 inducing peptides. The data set used in this study comprises 904 experimentally validated IL4 inducing and 742 noninducing MHC class II binders. Our analysis revealed that certain types of residues are preferred at certain positions in IL4 inducing peptides. It was also observed that IL4 inducing and noninducing epitopes differ in compositional and motif pattern. Based on our analysis we developed classification models where the hybrid method of amino acid pairs and motif information performed the best with maximum accuracy of 75.76% and MCC of 0.51. These results indicate that it is possible to predict IL4 inducing peptides with reasonable precession. These models would be useful in designing the peptides that may induce desired Th2 response.
Taxonomy and Polyphasic Characterization of Alkaline Amylase Producing Marine ActinomyceteStreptomyces rocheiBTSS 1001
Authors: Acharyabhatta Aparna , Kandula Siva Kumar , Terli Ramana
Published: December 2013

Actinomycetes isolated from marine sediments along the southeast coast of Bay of Bengal were investigated for amylolytic activity. Marine actinomycete BTSS 1001 producing an alkaline amylase was identified from marine sediment of Diviseema coast, Bay of Bengal. The isolate produced alkaline amylase with maximum amylolytic activity at pH 9.5 at 50°C. The organism produced white to pale grey substrate mycelium and grayish aerial mycelium with pinkish brown pigmentation. A comprehensive study of morphological, physiological parameters, cultural characteristics, and biochemical studies was performed. The presence of iso-C15 : 0, anteiso-C15 : 0, iso-C16 : 0, and anteiso-C17 : 0as the major cellular fatty acids, LL-diaminopimelic acid as the characteristic cell wall component, and menaquinones MK-9H(6)and MK-9H(8)as the major isoprenoid quinones is attributed to the strain BTSS 1001 belonging to the genusStreptomyces. Comparison of 16S rRNA gene sequences showed that strain BTSS 1001 exhibited the highest similarities to the type strains ofStreptomyces rochei(99%),Streptomyces plicatus(99%), andStreptomyces enissocaesilis(99%). Using the polyphasic taxonomical approach and phenotypic characteristic studies, the isolate BTSS 1001 was characterized as marine actinomyceteStreptomyces rochei.
Online Bridge Crack Monitoring with Smart Film
Authors: Zhang Benniu , Wang Shuliang , Li Xingxing , Zhou Zhixiang , Zhang Xu , Yang Guang , Qiu Minfeng
Published: December 2013

Smart film crack monitoring method, which can be used for detecting initiation, length, width, shape, location, and propagation of cracks on real bridges, is proposed. Firstly, the fabrication of the smart film is developed. Then the feasibility of the method is analyzed and verified by the mechanical sensing character of the smart film under the two conditions of normal strain and crack initiation. Meanwhile, the coupling interference between parallel enameled wires of the smart film is discussed, and then low‐frequency detecting signal and the custom communication protocol are used to decrease interference. On this basis, crack monitoring system with smart film is designed, where the collected crack data is sent to the remote monitoring center and the cracks are simulated and recurred. Finally, the monitoring system is applied to six bridges, and the effects are discussed.
Charged Hadron Multiplicity Distribution at Relativistic Heavy-Ion Colliders
Authors: Kumar Ashwini , Srivastava P. K. , Singh B. K. , Singh C. P.
Published: December 2013

The present paper reviews facts and problems concerning charge hadron production in high energy collisions. Main emphasis is laid on the qualitative and quantitative description of general characteristics and properties observed for charged hadrons produced in such high energy collisions. Various features of available experimental data, for example, the variations of charged hadron multiplicity and pseudorapidity density with the mass number of colliding nuclei, center-of-mass energies, and the collision centrality obtained from heavy-ion collider experiments, are interpreted in the context of various theoretical concepts and their implications. Finally, several important scaling features observed in the measurements mainly at RHIC and LHC experiments are highlighted in the view of these models to draw some insight regarding the particle production mechanism in heavy-ion collisions.