bluuebunny/crossref_metadata_2025 huggingface dataset:
Neutrophils Play an Important Role in Protective Immunity against Coxiella burnetii Infection
Authors: Elliott Alexandra , Schoenlaub Laura , Freches Danielle , Mitchell William , Zhang Guoquan
Published: May 2015

Coxiella burnetii
is an obligate intracellular Gram-negative bacterium that causes the zoonotic disease Q fever. Although Q fever is mainly transmitted by aerosol infection, study of the immune responses in the lung following pulmonary
C. burnetii
infection is lacking. Neutrophils are considered the first immune cell to migrate into the lung and play an important role in host defense against aerosol infection with microbial pathogens. However, the role of neutrophils in the host defense against
C. burnetii
infection remains unclear. To determine the role of neutrophils in protective immunity against
C. burnetii
infection, the RB6-8C5 antibody was used to deplete neutrophils in mice before intranasal infection with
C. burnetii
. The results indicated that neutrophil-depleted mice developed more severe disease than their wild-type counterparts, suggesting that neutrophils play an important role in host defense against
C. burnetii
pulmonary infection. We also found that neither CXC chemokine receptor 2 (CXCR2) nor interleukin-17 (IL-17) receptor (IL-17R) deficiency changed the severity of disease following intranasal
C. burnetii
challenge, suggesting that keratinocyte-derived chemokine and IL-17 may not play essential roles in the response to
C. burnetii
infection. However, significantly higher
C. burnetii
genome copy numbers were detected in the lungs of IL-1R
−/−
mice at 14 days postinfection. This indicates that IL-1 may be important for the clearance of
C. burnetii
from the lungs following intranasal infection. Our results also suggest that neutrophils are involved in protecting vaccinated mice from
C. burnetii
challenge-induced disease. This is the first study to demonstrate an important role for neutrophils in protective immunity against
C. burnetii
infection.
Transcriptome Reprogramming by Plasmid-Encoded Transcriptional Regulators Is Required for Host Niche Adaption of a Macrophage Pathogen
Authors: Coulson Garry B. , Miranda-CasoLuengo Aleksandra A. , Miranda-CasoLuengo Raúl , Wang Xiaoguang , Oliver Jenna , Willingham-Lane Jennifer M. , Meijer Wim G. , Hondalus Mary K.
Published: May 2015

Rhodococcus equi
is a facultative intracellular pathogen of macrophages, relying on the presence of a conjugative virulence plasmid harboring a 21-kb pathogenicity island (PAI) for growth in host macrophages. The PAI encodes a family of 6 virulence-associated proteins (Vaps) in addition to 20 other proteins. The contribution of these to virulence has remained unclear. We show that the presence of only 3 virulence plasmid genes (of 73 in total) is required and sufficient for intracellular growth. These include a single
vap
family member,
vapA
, and two PAI-located transcriptional regulators,
virR
and
virS
. Both transcriptional regulators are essential for wild-type-level expression of
vapA
, yet
vapA
expression alone is not sufficient to allow intracellular growth. A whole-genome microarray analysis revealed that VirR and VirS substantially integrate themselves into the chromosomal regulatory network, significantly altering the transcription of 18% of all chromosomal genes. This pathoadaptation involved significant enrichment of select gene ontologies, in particular, enrichment of genes involved in transport processes, energy production, and cellular metabolism, suggesting a major change in cell physiology allowing the bacterium to grow in the hostile environment of the host cell. The results suggest that following the acquisition of the virulence plasmid by an avirulent ancestor of
R. equi
, coevolution between the plasmid and the chromosome took place, allowing VirR and VirS to regulate the transcription of chromosomal genes in a process that ultimately promoted intracellular growth. Our findings suggest a mechanism for cooption of existing chromosomal traits during the evolution of a pathogenic bacterium from an avirulent saprophyte.
Intracellular Listeria monocytogenes Comprises a Minimal but Vital Fraction of the Intestinal Burden following Foodborne Infection
Authors: Jones Grant S. , Bussell Kate M. , Myers-Morales Tanya , Fieldhouse Abigail M. , Bou Ghanem Elsa N. , D'Orazio Sarah E. F.
Published: May 2015

Listeria monocytogenes
is a highly adaptive bacterium that replicates as a free-living saprophyte in the environment as well as a facultative intracellular pathogen that causes invasive foodborne infections. The intracellular life cycle of
L. monocytogenes
is considered to be its primary virulence determinant during mammalian infection; however, the proportion of
L. monocytogenes
that is intracellular
in vivo
has not been studied extensively. In this report, we demonstrate that the majority of wild-type (strain EGDe) and mouse-adapted (InlA
m
-expressing)
L. monocytogenes
recovered from the mesenteric lymph nodes (MLN) was extracellular within the first few days after foodborne infection. In addition, significantly lower burdens of
L. monocytogenes
were recovered from the colon, spleen, and liver of gentamicin-treated mice than of control mice. This led us to investigate whether intracellular replication of
L. monocytogenes
was essential during the intestinal phase of infection. We found that lipoate protein ligase-deficient
L. monocytogenes
(Δ
lplA1
) mutants, which display impaired intracellular growth, were able to colonize the colon but did not persist efficiently and had a significant defect in spreading to the MLN, spleen, and liver. Together, these data indicate that the majority of the
L. monocytogenes
burden in the gastrointestinal tract is extracellular, but the small proportion of intracellular
L. monocytogenes
is essential for dissemination to the MLN and systemic organs.
Chlamydial Variants Differ in Ability To Ascend the Genital Tract in the Guinea Pig Model of Chlamydial Genital Infection
Authors: Yeruva Laxmi , Bowlin Anne K. , Spencer Nicole , Maurelli Anthony T. , Rank Roger G.
Published: May 2015

An important question in the study of chlamydial genital tract disease is why some women develop severe upper tract disease while others have mild or even “silent” infections with or without pathology. Animal studies suggest that the pathological outcome of an infection is dependent upon both the composition of the infecting chlamydial population and the genotype of the host, along with host physiological effects, such as the cyclical production of reproductive hormones and even the size of the infecting inoculum or the number of repeated infections. In this study, we compared two variants of
Chlamydia caviae
, contrasting in virulence, with respect to their abilities to ascend the guinea pig genital tract. We then determined the effect of combining the two variants on the course of infection and on the bacterial loads of the two variants in the genital tract. Although the variants individually had similar infection kinetics in the cervix, SP6, the virulent variant, could be isolated from the oviducts more often and in greater numbers than the attenuated variant, AZ2. SP6 also elicited higher levels of interleukin 8 (IL-8) in the lower genital tract and increased leukocyte infiltration in the cervix and uterus compared to AZ2. When the two variants were combined in a mixed infection, SP6 outcompeted AZ2 in the lower genital tract; however, AZ2 was able to ascend the genital tract as readily as SP6. These data suggest that the ability of SP6 to elicit an inflammatory response in the lower genital tract facilitates the spread of both variants to the oviducts.
The Crystal Structure of Nitrosomonas europaea Sucrose Synthase Reveals Critical Conformational Changes and Insights into Sucrose Metabolism in Prokaryotes
Authors: Wu Rui , Asención Diez Matías D. , Figueroa Carlos M. , Machtey Matías , Iglesias Alberto A. , Ballicora Miguel A. , Liu Dali
Published: May 2015

In this paper we report the first crystal structure of a prokaryotic sucrose synthase from the nonphotosynthetic bacterium
Nitrosomonas europaea
. The obtained structure was in an open form, whereas the only other available structure, from the plant
Arabidopsis thaliana
, was in a closed conformation. Comparative structural analysis revealed a “hinge-latch” combination, which is critical to transition between the open and closed forms of the enzyme. The
N. europaea
sucrose synthase shares the same fold as the GT-B family of the retaining glycosyltransferases. In addition, a triad of conserved homologous catalytic residues in the family was shown to be functionally critical in the
N. europaea
sucrose synthase (Arg567, Lys572, and Glu663). This implies that sucrose synthase shares not only a common origin with the GT-B family but also a similar catalytic mechanism. The enzyme preferred transferring glucose from ADP-glucose rather than UDP-glucose like the eukaryotic counterparts. This predicts that these prokaryotic organisms have a different sucrose metabolic scenario from plants. Nucleotide preference determines where the glucose moiety is targeted after sucrose is degraded.

IMPORTANCE
We obtained biochemical and structural evidence of sucrose metabolism in nonphotosynthetic bacteria. Until now, only sucrose synthases from photosynthetic organisms have been characterized. Here, we provide the crystal structure of the sucrose synthase from the chemolithoautotroph
N. europaea
. The structure supported that the enzyme functions with an open/close induced fit mechanism. The enzyme prefers as the substrate adenine-based nucleotides rather than uridine-based like the eukaryotic counterparts, implying a strong connection between sucrose and glycogen metabolism in these bacteria. Mutagenesis data showed that the catalytic mechanism must be conserved not only in sucrose synthases but also in all other retaining GT-B glycosyltransferases.
Phase-Variable Control of Multiple Phenotypes in Acinetobacter baumannii Strain AB5075
Authors: Tipton Kyle A. , Dimitrova Daniela , Rather Philip N.
Published: May 2015

Acinetobacter baumannii
strain AB5075 produces colonies with two opacity phenotypes, designated opaque and translucent. These phenotypes were unstable and opaque and translucent colony variants were observed to interconvert at high frequency, suggesting that a phase-variable mechanism was responsible. The frequency of phase variation both within colonies and in broth cultures increased in a cell density-dependent manner and was mediated by the accumulation of an extracellular factor. This factor was distinct from the known
A. baumannii
signaling molecule 3-OH C
12
-homoserine lactone. Opaque and translucent colony variants exhibited a number of phenotypic differences, including cell morphology, surface motility, biofilm formation, antibiotic resistance, and virulence in a
Galleria mellonella
model. Additional clinical isolates exhibited a similar phase-variable control of colony opacity, suggesting that this may be a common feature of
A. baumannii
.

IMPORTANCE
A novel phase-variable mechanism has been identified in
Acinetobacter baumannii
that results in an interconversion between opaque and translucent colony phenotypes. This phase variation also coordinately regulates motility, cell shape, biofilm formation, antibiotic resistance, and virulence. The frequency of phase variation is increased at high cell density via a diffusible extracellular signal. To our knowledge, this report presents the first example of phase variation in
A. baumannii
and also the first example of quorum sensing-mediated control of phase variation in a bacterium. The findings are important, as this phase-variable mechanism can be identified only via changes in colony opacity using oblique light; therefore, many researchers studying
A. baumannii
may unknowingly be working with different colony variants.
Cofactor Specificity of the Bifunctional Alcohol and Aldehyde Dehydrogenase (AdhE) in Wild-Type and Mutant Clostridium thermocellum and Thermoanaerobacteriumsaccharolyticum
Authors: Zheng Tianyong , Olson Daniel G. , Tian Liang , Bomble Yannick J. , Himmel Michael E. , Lo Jonathan , Hon Shuen , Shaw A. Joe , van Dijken Johannes P. , Lynd Lee R.
Published: May 2015

Clostridium thermocellum
and
Thermoanaerobacterium
saccharolyticum
are thermophilic bacteria that have been engineered to produce ethanol from the cellulose and hemicellulose fractions of biomass, respectively. Although engineered strains of
T. saccharolyticum
produce ethanol with a yield of 90% of the theoretical maximum, engineered strains of
C. thermocellum
produce ethanol at lower yields (∼50% of the theoretical maximum). In the course of engineering these strains, a number of mutations have been discovered in their
adhE
genes, which encode both alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH) enzymes. To understand the effects of these mutations, the
adhE
genes from six strains of
C. thermocellum
and
T. saccharolyticum
were cloned and expressed in
Escherichia coli
, the enzymes produced were purified by affinity chromatography, and enzyme activity was measured. In wild-type strains of both organisms, NADH was the preferred cofactor for both ALDH and ADH activities. In high-ethanol-producing (ethanologen) strains of
T. saccharolyticum
, both ALDH and ADH activities showed increased NADPH-linked activity. Interestingly, the AdhE protein of the ethanologenic strain of
C. thermocellum
has acquired high NADPH-linked ADH activity while maintaining NADH-linked ALDH and ADH activities at wild-type levels. When single amino acid mutations in AdhE that caused increased NADPH-linked ADH activity were introduced into
C. thermocellum
and
T. saccharolyticum
, ethanol production increased in both organisms. Structural analysis of the wild-type and mutant AdhE proteins was performed to provide explanations for the cofactor specificity change on a molecular level.

IMPORTANCE
This work describes the characterization of the AdhE enzyme from different strains of
C. thermocellum
and
T. saccharolyticum
.
C. thermocellum
and
T. saccharolyticum
are thermophilic anaerobes that have been engineered to make high yields of ethanol and can solubilize components of plant biomass and ferment the sugars to ethanol. In the course of engineering these strains, several mutations arose in the bifunctional ADH/ALDH protein AdhE, changing both enzyme activity and cofactor specificity. We show that changing AdhE cofactor specificity from mostly NADH linked to mostly NADPH linked resulted in higher ethanol production by
C. thermocellum
and
T. saccharolyticum
.
A Trigger Residue for Transmembrane Signaling in the Escherichia coli Serine Chemoreceptor
Authors: Kitanovic Smiljka , Ames Peter , Parkinson John S.
Published: May 2015

The transmembrane Tsr protein of
Escherichia coli
mediates chemotactic responses to environmental serine gradients. Serine binds to the periplasmic domain of the homodimeric Tsr molecule, promoting a small inward displacement of one transmembrane helix (TM2). TM2 piston displacements, in turn, modulate the structural stability of the Tsr-HAMP domain on the cytoplasmic side of the membrane to control the autophosphorylation activity of the signaling CheA kinase bound to the membrane-distal cytoplasmic tip of Tsr. A five-residue control cable segment connects TM2 to the AS1 helix of HAMP and transmits stimulus and sensory adaptation signals between them. To explore the possible role of control cable helicity in transmembrane signaling by Tsr, we characterized the signaling properties of mutant receptors with various control cable alterations. An all-alanine control cable shifted Tsr output toward the kinase-on state, whereas an all-glycine control cable prevented Tsr from reaching either a fully on or fully off output state. Restoration of the native isoleucine (I214) in these synthetic control cables largely alleviated their signaling defects. Single amino acid replacements at Tsr-I214 shifted output toward the kinase-off (L, N, H, and R) or kinase-on (A and G) states, whereas other control cable residues tolerated most amino acid replacements with little change in signaling behavior. These findings indicate that changes in control cable helicity might mediate transitions between the kinase-on and kinase-off states during transmembrane signaling by chemoreceptors. Moreover, the Tsr-I214 side chain plays a key role, possibly through interaction with the membrane interfacial environment, in triggering signaling changes in response to TM2 piston displacements.

IMPORTANCE
The Tsr protein of
E. coli
mediates chemotactic responses to environmental serine gradients. Stimulus signals from the Tsr periplasmic sensing domain reach its cytoplasmic kinase control domain through piston displacements of a membrane-spanning helix and an adjoining five-residue control cable segment. We characterized the signaling properties of Tsr variants to elucidate the transmembrane signaling role of the control cable, an element present in many microbial sensory proteins. Both the kinase-on and kinase-off output states of Tsr depended on control cable helicity, but only one residue, I214, was critical for triggering responses to attractant inputs. These findings suggest that signal transmission in Tsr involves modulation of control cable helicity through interaction of the I214 side chain with the cytoplasmic membrane.
Secreted Cyclic Di-GMP Induces Stalk Cell Differentiation in the Eukaryote Dictyostelium discoideum
Authors: Chen Zhi-hui , Schaap Pauline
Published: May 2015

Cyclic di-GMP (c-di-GMP) is currently recognized as the most widely used intracellular signal molecule in prokaryotes, but roles in eukaryotes were only recently discovered. In the social amoeba
Dictyostelium discoideum
, c-di-GMP, produced by a prokaryote-type diguanylate cyclase, induces the differentiation of stalk cells, thereby enabling the formation of spore-bearing fruiting bodies. In this review, we summarize the currently known mechanisms that control the major life cycle transitions of
Dictyostelium
and focus particularly on the role of c-di-GMP in stalk formation. Stalk cell differentiation has characteristics of autophagic cell death, a process that also occurs in higher eukaryotes. We discuss the respective roles of c-di-GMP and of another signal molecule, differentiation-inducing factor 1, in autophagic cell death
in vitro
and in stalk formation
in vivo
.
Temporal Hierarchy of Gene Expression Mediated by Transcription Factor Binding Affinity and Activation Dynamics
Authors: Gao Rong , Stock Ann M.
Published: May 2015

Understanding cellular responses to environmental stimuli requires not only the knowledge of specific regulatory components but also the quantitative characterization of the magnitude and timing of regulatory events. The two-component system is one of the major prokaryotic signaling schemes and is the focus of extensive interest in quantitative modeling and investigation of signaling dynamics. Here we report how the binding affinity of the PhoB two-component response regulator (RR) to target promoters impacts the level and timing of expression of PhoB-regulated genes. Information content has often been used to assess the degree of conservation for transcription factor (TF)-binding sites. We show that increasing the information content of PhoB-binding sites in designed
phoA
promoters increased the binding affinity and that the binding affinity and concentration of phosphorylated PhoB (PhoB~P) together dictate the level and timing of expression of
phoA
promoter variants. For various PhoB-regulated promoters with distinct promoter architectures, expression levels appear not to be correlated with TF-binding affinities, in contrast to the intuitive and oversimplified assumption that promoters with higher affinity for a TF tend to have higher expression levels. However, the expression timing of the core set of PhoB-regulated genes correlates well with the binding affinity of PhoB~P to individual promoters and the temporal hierarchy of gene expression appears to be related to the function of gene products during the phosphate starvation response. Modulation of the information content and binding affinity of TF-binding sites may be a common strategy for temporal programming of the expression profile of RR-regulated genes.

IMPORTANCE
A single TF often orchestrates the expression of multiple genes in response to environmental stimuli. It is not clear how different TF-binding sites within the regulon dictate the expression profile. Our studies of
Escherichia coli
PhoB, a response regulator that controls expression of a core set of phosphate assimilation genes in response to phosphate starvation, showed that expression levels of PhoB-regulated genes are under sophisticated control and do not follow a simple correlation with the binding affinity of PhoB~P to individual promoters. However, the expression timing correlates with the PhoB-binding affinity and gene functions. Genes involved in direct P
i
uptake contain high-affinity sites and are transcribed earlier than genes involved in phosphorus scavenging. This illustrates an elaborate mechanism of temporally programmed gene expression, even for nondevelopmental pathways.
Better estimation of origin–destination matrix using automated intersection movement count data
Authors: Tuydes-Yaman Hediye , Altintasi Oruc , Sendil Nuri
Published: May 2015

Intersection movements carry more disaggregate information about origin–destination (O–D) flows than link counts in a traffic network. In this paper, a mathematical formulation is presented for O–D matrix estimation using intersection counts, which is based on an existing linear programming model employing link counts. The proposed model estimates static O–D flows for uncongested networks assuming no a priori information on the O–D matrix. Both models were tested in two hypothetical networks previously used in O–D matrix studies to monitor their performances assuming various numbers of count location and measurement errors. Two new measures were proposed to evaluate the model characteristics of O–D flow estimation using traffic counts. While both link count based and intersection count based models performed with the same success under complete data collection assumption, intersection count based formulation estimated the O–D flows more successfully under decreasing number of observation locations. Also, the results of the 30 measurement error scenarios revealed that it performs more robustly than the link count based one; thus, it better estimates the O–D flows.
Simulation study of traffic car accidents at a single lane roundabout
Authors: Echab H. , Lakouari N. , Ez-Zahraouy H. , Benyoussef A.
Published: May 2015

In this paper, using the Nagel-Schreckenberg model, we numerically investigate the probability [Formula: see text] of entering/circulating car accidents to occur at single-lane roundabout under the expanded open boundary. The roundabout consists of N on-ramps (respectively, off-ramps). The boundary is controlled by the injecting rates [Formula: see text] and the extracting rate [Formula: see text]. The simulation results show that, depending on the injecting rates, the car accidents are more likely to happen when the capacity of the rotary is set to its maximum. Moreover, we found that the large values of rotary size L and the probability of preferential [Formula: see text] are reliable to improve safety and reduce accidents. However, the usage of indicator, the increase of [Formula: see text] and/or N provokes an increase of car accident probability.
On the Variability of the Sound Transmission Loss of Composite Panels Through a Parametric Probabilistic Approach
Authors: Ben Souf M. A. , Chronopoulos D. , Ichchou M. , Bareille O. , Haddar M.
Published: May 2015

A robust model for the prediction of the variability of the vibro-acoustic response is presented in this paper. The dynamic response of composite panels is treated using a Statistical Energy Analysis (SEA) approach. One of the basic input parameters is the propagating flexural wavenumber of the modeled panel. The Wave Finite Element Method (WFEM) is used to investigate the dispersion characteristics of the layered panel. It is based on the evaluation of the mass and the stiffness matrices of a periodic segment of the structure. A polynomial eigenvalue problem is then formed for calculating the wavenumbers and the wave mode shapes. The main novelty in this paper consists in evaluating the influence of the variability of the mechanical parameters of the composite panel on its vibro-acoustic response, that is on its sound transmission loss (STL). This influence is quantified using the generalized polynomial chaos expansion. The efficiency of the approach is exhibited for isotropic and orthotropic panels.
A review on out-of-sequence deformation in the Himalaya
Authors: Mukherjee Soumyajit
Published: May 2015

Out-of-sequence deformation in the Himalaya has been caused mainly by thrusting. Out-of-sequence thrusts, usually north- to NE-dipping foreshear planes, occur inside the Sub-Himalaya (SH), Lesser Himalaya (LH) and Greater Himalayan Crystalline (GHC) sequences. Where absolute dates are available, the youngest slip within the SH occurred near the Janauri Anticline (India) at
c.
AD 1400–1460. The Munsiari Thrust (India) activated within the LH at
c.
1–2 Ma and the Main Central Thrust zone in the Marsyandi valley (Nepal) in the GHC was formed during the Holocene (
c.
0.3 ka). Except for the Riasi Thrust (Kashmir, India), the Paonta Thrust (Himachal Pradesh, India) in the Siwalik and the Tons Thrust (Garhwal region, India) within the Main Central Thrust zone, crustal shortening related to out-of-sequence thrusting in the Himalaya has been insignificant. The major litho-/stratigraphic contacts within the SH and the GHC at some places acted as out-of-sequence thrusts. Out-of-sequence thrusts in the SH have been detected mainly based on geomorphological observations. However, more quantitative geochronological studies have detected out-of-sequence thrusting from
c.
22 Ma up to Holocene age in the GHC based on age jumps, especially within the Main Central Thrust zone. Crustal channel flow (specifically for the GHC) and/or the critical taper model with or without erosion can be used to explain the Himalayan out-of-sequence thrusts.
The Challenges of Using Biodata in Promotional Filmmaking
Authors: Reeves Stuart , Martindale Sarah , Tennent Paul , Benford Steve , Marshall Joe , Walker Brendan
Published: May 2015

We present a study of how filmmakers collected and visualized physiological data—“biodata”—to construct a series of short promotional films depicting people undergoing “thrilling” experiences. Drawing on ethnographic studies of two major advertising campaigns, we highlight key concerns for integrating sensors and sensor data into film production. Our findings address the perceived benefits of using biodata within narratives; the nature of different on-screen representations of biodata; and the challenges presented when integrating biodata into production processes. Drawing on this, we reconsider the nature of information visualization in the filmmaking context. Further implications from our case studies provide recommendations for human--computer interaction (HCI) collaborations with filmmaking and broadcast industries, focusing both on the practical matters of fitting sensor technologies into and handling data within production workflows, as well as discussing the broader implications for managing the veracity of that data within professional media production.
Partitioned Global Address Space Languages
Authors: De Wael Mattias , Marr Stefan , De Fraine Bruno , Van Cutsem Tom , De Meuter Wolfgang
Published: May 2015

The Partitioned Global Address Space (PGAS) model is a parallel programming model that aims to improve programmer productivity while at the same time aiming for high performance. The main premise of PGAS is that a globally shared address space improves productivity, but that a distinction between local and remote data accesses is required to allow performance optimizations and to support scalability on large-scale parallel architectures. To this end, PGAS preserves the global address space while embracing awareness of nonuniform communication costs.

Today, about a dozen languages exist that adhere to the PGAS model. This survey proposes a definition and a taxonomy along four axes: how parallelism is introduced, how the address space is partitioned, how data is distributed among the partitions, and finally, how data is accessed across partitions. Our taxonomy reveals that today’s PGAS languages focus on distributing regular data and distinguish only between local and remote data access cost, whereas the distribution of irregular data and the adoption of richer data access cost models remain open challenges.
Assessing the Structural Complexity of Computer and Communication Networks
Authors: Kamisiński Andrzej , Chołda Piotr , Jajszczyk Andrzej
Published: May 2015

In this tutorial, 17 structural complexity indices are presented and compared, each representing one of the following categories: adjacency- and distance-based metrics, Shannon entropy-based metrics, product measures, subgraph-based metrics, and path- and walk-based metrics. The applicability of these indices to computer and communication networks is evaluated with the aid of different elementary, specifically designed, random, and real network topologies. On the grounds of the evaluation study, advantages and disadvantages of particular metrics are identified. In addition, their general properties and runtimes are assessed, and a general view on the structural network complexity is presented.
Energy-Efficient Networking Solutions in Cloud-Based Environments
Authors: Moghaddam Fahimeh Alizadeh , Lago Patricia , Grosso Paola
Published: May 2015

The energy consumed by data centers hosting cloud services is increasing enormously. This brings the need to reduce energy consumption of different components in data centers. In this work, we focus on energy efficiency of the networking component. However, how different networking solutions impact energy consumption is still an open question. We investigate the state of the art in energy-efficient networking solutions in cloud-based environments. We follow a systematic literature review method to select primary studies. We create a metamodel based on the codes extracted from our primary studies using the Coding analytical method. Our findings show three abstraction levels of the proposed networking solutions to achieve energy efficiency in cloud-based environments: Strategy, Solution, and Technology. We study the historical trends in the investigated solutions and conclude that the emerging and most widely adopted one is the
Decision framework
.
Deletion of the Rab GAP Tbc1d1 modifies glucose, lipid, and energy homeostasis in mice
Authors: Hargett Stefan R. , Walker Natalie N. , Hussain Syed S. , Hoehn Kyle L. , Keller Susanna R.
Published: May 2015

Tbc1d1 is a Rab GTPase-activating protein (GAP) implicated in regulating intracellular retention and cell surface localization of the glucose transporter GLUT4 and thus glucose uptake in a phosphorylation-dependent manner. Tbc1d1 is most abundant in skeletal muscle but is expressed at varying levels among different skeletal muscles. Previous studies with male Tbc1d1-deficient (Tbc1d1−/−) mice on standard and high-fat diets established a role for Tbc1d1 in glucose, lipid, and energy homeostasis. Here we describe similar, but also additional abnormalities in male and female Tbc1d1−/− mice. We corroborate that Tbc1d1 loss leads to skeletal muscle-specific and skeletal muscle type-dependent abnormalities in GLUT4 expression and glucose uptake in female and male mice. Using subcellular fractionation, we show that Tbc1d1 controls basal intracellular GLUT4 retention in large skeletal muscles. However, cell surface labeling of extensor digitorum longus muscle indicates that Tbc1d1 does not regulate basal GLUT4 cell surface exposure as previously suggested. Consistent with earlier observations, female and male Tbc1d1−/− mice demonstrate increased energy expenditure and skeletal muscle fatty acid oxidation. Interestingly, we observe sex-dependent differences in in vivo phenotypes. Female, but not male, Tbc1d1−/− mice have decreased body weight and impaired glucose and insulin tolerance, but only male Tbc1d1−/− mice show increased lipid clearance after oil gavage. We surmise that similar changes at the tissue level cause differences in whole-body metabolism between male and female Tbc1d1−/− mice and between male Tbc1d1−/− mice in different studies due to variations in body composition and nutrient handling.
Imidazoline-like drugs improve insulin sensitivity through peripheral stimulation of adiponectin and AMPK pathways in a rat model of glucose intolerance
Authors: Weiss Maud , Bouchoucha Soumaya , Aiad Farouk , Ayme-Dietrich Estelle , Dali-Youcef Nassim , Bousquet Pascal , Greney Hugues , Niederhoffer Nathalie
Published: May 2015

Altered adiponectin signaling and chronic sympathetic hyperactivity have both been proposed as key factors in the pathogenesis of metabolic syndrome. We recently reported that activation of I1imidazoline receptors (I1R) improves several symptoms of the metabolic syndrome through sympathoinhibition and increases adiponectin plasma levels in a rat model of metabolic syndrome (Fellmann L, Regnault V, Greney H, et al. J Pharmacol Exp Ther 346: 370–380, 2013). The present study was designed to explore the peripheral component of the beneficial actions of I1R ligands (i.e., sympathoinhibitory independent effects). Aged rats displaying insulin resistance and glucose intolerance were treated with LNP509, a peripherally acting I1R agonist. Glucose tolerance, insulin sensitivity, and adiponectin signaling were assessed at the end of the treatment. Direct actions of the ligand on hepatocyte and adipocyte signaling were also studied. LNP509 reduced the area under the curve of the intravenous glucose tolerance test and enhanced insulin hypoglycemic action and intracellular signaling (Akt phosphorylation), indicating improved glucose tolerance and insulin sensitivity. LNP509 stimulated adiponectin secretion acting at I1R on adipocytes, resulting in increased plasma levels of adiponectin; it also enhanced AMPK phosphorylation in hepatic tissues. Additionally, I1R activation on hepatocytes directly enhanced AMPK phosphorylation. To conclude, I1R ligands can improve insulin sensitivity acting peripherally, independently of sympathoinhibition; stimulation of adiponectin and AMPK pathways at insulin target tissues may account for this effect. This may open a promising new way for the treatment of the metabolic syndrome.
Acute effects of hyperinsulinemia and hyperglycemia on vascular inflammatory biomarkers and endothelial function in overweight and obese humans
Authors: Perkins Jennifer M. , Joy Nino G. , Tate Donna B. , Davis Stephen N.
Published: May 2015

We investigated the separate and combined effects of hyperglycemia and hyperinsulinemia on markers of endothelial function, proinflammatory and proatherothrombotic responses in overweight/obese nondiabetic humans. Twenty-two individuals (13 F/9 M, BMI 30.1 ± 4.1 kg/m2) were studied during four randomized, single-blind protocols. The pancreatic clamp technique was combined with 4-h glucose clamps consisting of either 1) euinsulinemia-euglycemia, 2) euinsulinemia-hyperglycemia, 3) hyperinsulinemia-hyperglycemia, or 4) hyperinsulinemia-euglycemia. Insulin levels were higher (998 ± 66 vs. 194 ± 22 pmol/l) during hyperinsulinemia compared with euinsulinemia. Glucose levels were 11.1 mmol/l during hyperinsulinemia compared with 5.1 ± 0.1 mmol/l during euglycemia. VCAM, ICAM, P-selectin, E-selectin, IL-6, adiponectin, and PAI-1 responses were all increased ( P < 0.01-0.0001), and endothelial function was decreased ( P < 0.0005) during euinsulinemia-hyperglycemia compared with other protocols. Hyperinsulinemia in the presence of hyperglycemia prevented the increase in proinflammatory and proatherothrombotic markers while also normalizing vascular endothelial function. We conclude that 4 h of moderate hyperglycemia can result in increases of proinflammatory markers (ICAM, VCAM, IL-6, E-selectin), platelet activation (P-selectin), reduced fibrinolytic balance (increased PAI-1), and disordered endothelial function in a group of obese and overweight individuals. Hyperinsulinemia prevents the actions of moderate hyperglycemia to reduce endothelial function and increase proinflammatory and proatherothrombotic markers.
Insulin secretion and signaling in response to dietary restriction and subsequent re-alimentation in cattle
Authors: Keogh Kate , Kenny David A. , Kelly Alan K. , Waters Sinéad M.
Published: May 2015

The objectives of this study were to examine systemic insulin response to a glucose tolerance test (GTT) and transcript abundance of genes of the insulin signaling pathway in skeletal muscle, during both dietary restriction and re-alimentation-induced compensatory growth. Holstein Friesian bulls were blocked to one of two groups: 1) restricted feed allowance for 125 days ( period 1) (RES, n = 15) followed by ad libitum feeding for 55 days ( period 2) or 2) ad libitum access to feed throughout (periods 1 and 2) (ADLIB, n = 15). On days 90 and 36 of periods 1 and 2, respectively, a GTT was performed. M. longissimus dorsi biopsies were harvested from all bulls on days 120 and 15 of periods 1 and 2, respectively, and RNA-Seq analysis was performed. RES displayed a lower growth rate during period 1 (RES: 0.6 kg/day, ADLIB: 1.9 kg/day; P < 0.001), subsequently gaining more during re-alimentation (RES: 2.5 kg/day, ADLIB: 1.4 kg/day; P < 0.001). Systemic insulin response to glucose administration was lower in RES in period 1 ( P < 0.001) with no difference observed during period 2. The insulin signaling pathway in M. longissimus dorsi was enriched ( P < 0.05) in response to dietary restriction but not during re-alimentation ( P > 0.05). Genes differentially expressed in the insulin signaling pathway suggested a greater sensitivity to insulin in skeletal muscle, with pleiotropic effects of insulin signaling interrupted during dietary restriction. Collectively, these results indicate increased sensitivity to glucose clearance and skeletal muscle insulin signaling during dietary restriction; however, no overall role for insulin was apparent in expressing compensatory growth.
Fabrication of PANI/C‐TiO2 Composite Nanotube Arrays Electrode for Supercapacitor
Authors: Zhang Chengcheng , Peng Changjian , Gao Biao , Peng Xiang , Zhang Xuming , Tao Jingyuan , Kong Jinhan , Fu Jijiang
Published: May 2015

Polyaniline/carbon doped TiO2 composite nanotube arrays (PANI/C‐TiO2 NTAs) have been prepared successfully by electrodepositing PANI in C‐TiO2 NTAs which were prepared by directly annealing the as‐anodized TiO2 NTAs under Ar atmosphere. The organic residual in the TiO2 NTAs during the process of anodization acts as carbon source and is carbonized in Ar atmosphere to manufacture the C‐TiO2 NTAs. The specific capacitance of the PANI/C‐TiO2 electrode is 120.8 mF cm−2 at a current density of 0.1 mA cm−2 and remains 104.3 mF cm−2 at a current density of 2 mA cm−2 with the calculated rate performance of 86.3%. After 5000 times of charge‐discharge cycling at a current density of 0.2 mA cm−2, the specific capacitance retains 88.7% compared to the first cycle. All these outstanding performances of the as‐prepared PANI/C‐TiO2 NTAs indicate it will be a promising electrode for supercapacitor.
Sample-Based Extreme Learning Machine with Missing Data
Authors: Gao Hang , Liu Xin-Wang , Peng Yu-Xing , Jian Song-Lei
Published: May 2015

Extreme learning machine (ELM) has been extensively studied in machine learning community during the last few decades due to its high efficiency and the unification of classification, regression, and so forth. Though bearing such merits, existing ELM algorithms cannot efficiently handle the issue of missing data, which is relatively common in practical applications. The problem of missing data is commonly handled by imputation (i.e., replacing missing values with substituted values according to available information). However, imputation methods are not always effective. In this paper, we propose a sample-based learning framework to address this issue. Based on this framework, we develop two sample-based ELM algorithms for classification and regression, respectively. Comprehensive experiments have been conducted in synthetic data sets, UCI benchmark data sets, and a real world fingerprint image data set. As indicated, without introducing extra computational complexity, the proposed algorithms do more accurate and stable learning than other state-of-the-art ones, especially in the case of higher missing ratio.
Enhancement of Gas Sensing Characteristics of Multiwalled Carbon Nanotubes by CF4 Plasma Treatment for SF6 Decomposition Component Detection
Authors: Zhang Xiaoxing , Wu Xiaoqing , Yang Bing , Xiao Hanyan
Published: May 2015

H2S and SO2 are important gas components of decomposed SF6 of partial discharge generated by insulation defects in gas‐insulated switchgear (GIS). Therefore, H2S and SO2 detection is important in the state evaluation and fault diagnosis of GIS. In this study, dielectric barrier discharge was used to generate CF4 plasma and modify multiwalled carbon nanotubes (MWNTs). The nanotubes were plasma‐treated at optimum discharge conditions under different treatment times (0.5, 1, 2, 5, 8, 10, and 12 min). Pristine and treated MWNTs were used as gas sensors to detect H2S and SO2. The effects of treatment time on gas sensitivity were analyzed. Results showed that the sensitivity, response, and recovery time of modified MWNTs to H2S were improved, but the recovery time of SO2 was almost unchanged. At 10 min treatment time, the MWNTs showed good stability and reproducibility with better gas sensing properties compared with the other nanotubes.
Relation of Reported Sedation and Ventilator Weaning Practices to Ventilator Time in Norwegian Intensive Care Units
Authors: Bekkevold Marit , Kvåle Reidar , Brattebø Guttorm
Published: May 2015

Background. Guidelines for sedation, ventilator weaning, and delirium screening are helpful to avoid too deep sedation and to identify signs of delirium in the intensive care unit (ICU). Methods. National ICU registry members (n=37) were surveyed regarding use of scoring instruments and guidelines for sedation and ventilator weaning, choice of drugs, and daily sedation interruption practices. Results were merged with registry data on ventilator time and length of stay for ICU patients ventilated >24 hours (7.075 ICU stays). Results. Eighty-five percent of the 33 responding ICUs used sedation scales and 39% and 55% had sedation and weaning protocols, respectively. An association was found between using protocols and longer mean ventilator time and mean length of ICU stay. Thirty three percent (11/33) practiced daily sedation interruption. Regular delirium assessment was associated with significantly shorter mean ventilator time and mean length of ICU stay but used by few. Conclusion. More ICUs had guidelines for weaning than for sedation. The ventilator time and length of ICU stay compared well with other studies. Although having guidelines was associated with longer ventilator time and ICU stay, the differences were rather small. Daily sedation interruption was seldom used. Few units used delirium scoring instruments.
A Proposed Maneuver to Guide Transseptal Puncture Using Real-Time Three-Dimensional Transesophageal Echocardiography: Pilot Study
Authors: Mahmoud Hani M. , Al-Ghamdi Mohammed A. , Ghabashi Abdullah E. , Anwar Ashraf M.
Published: May 2015

Aim of Study. To assess the feasibility of a new proposed maneuver “RATLe-90” using real-time three-dimensional transesophageal echocardiography (RT-3DTEE) for anatomically oriented visualization of the interatrial septum (IAS) in guiding the transseptal puncture TSP.Methods. The study included 20 patients (mean age,60.2±6.7years; 60% males) who underwent TSP for different indications. RT-3DTEE was used to guide TSP. The proposed maneuver RATLe-90 (Rotate-Anticlockwise-Tilt-Left-90) was applied in all cases to have the anatomically oriented en face view of the IAS from the right atrial (RA) aspect. Having this anatomically oriented view, we guided the TSP catheter towards the proper puncture site according to the planned procedure. Results. Using the RATLe-90 maneuver, the anatomically oriented en face view of the IAS from the RA was obtained in all patients. We were able to guide the puncture catheter to the proper puncture site on the IAS. The 3D images obtained were clearly understood by both echocardiographers and interventionists. The RATLe-90 maneuver acquisition time was19.9±1.6seconds. The time-to-tent was64.8±16.3seconds. Less TEE probe manipulations were needed while guiding the TSP.Conclusions. Application of RT3D-TEE during TSP using RATLe-90 maneuver is feasible with shorter fluoroscopy time and minimizing TEE probe manipulations.
Bilateral Adrenal Incidentalomas: A Rare Presentation of Lung Cancer
Authors: Diri Halit , Kiziltepe Melih , Karaburgu Sulbiye , Koc Mehmet Sait , Ozaslan Ersin , Tanriverdi Fatih
Published: May 2015

Adrenal incidentalomas are found incidentally during a radiologic examination performed for indications other than an adrenal disease, and 15% of them are bilateral adrenal masses. This study describes a 51-year-old male smoker patient admitted with diabetes mellitus. An abdominal ultrasonography performed due to his anemia revealed bilateral adrenal masses. His chest X-ray showed abnormal 10 cm opacity at the right upper lung, and brain, thorax, and abdomen CT scans showed multiple lesions compatible with lung cancer metastases. The pathological examination of the transthoracic lung biopsy specimen was consistent with lung adenocarcinoma. Findings in this patient indicate that, in middle aged patients with bilateral adrenal mass and a history or finding of any malignancy, the first diagnosis which should be considered is adrenal metastasis, and confirming the diagnosis by adrenal biopsy may be useless. Furthermore, screening all smoking patients by chest X-ray or thoracic CT for lung cancer may not be accepted as a routine procedure, but in smokers admitted to a hospital due to signs and symptoms attributed to a pulmonary disease, at least a chest X-ray should be requested.
Metal Content and Stable Isotope Determination in Some Commercial Beers from Romanian Markets
Authors: Voica Cezara , Magdas Dana-Alina , Feher Ioana
Published: May 2015

Characterization of beer samples is of interest because their compositions affect the taste and stability of beer and, also, consumer health. In this work, the characterizations of 20 Romanian beers were performed by mean of Inductively Coupled Plasma Mass Spectrometry (ICP-MS) and Isotope Ratio Mass Spectrometry (IRMS) in order to trace heavy metals and isotopic content of them. Major, minor, and trace metals are important in beer fermentation since they supply the appropriate environment for yeast growth and influence yeast metabolism. Beside this, the presence of the C4plants in the brewing process was followed. Our study has shown that the analyzed beers indicated the presence of different plant types used in brewing: C3, C3-C4mixtures, and also C4, depending on producers. Also the trace metal content of each sample is presented and discussed in this study. A comparison of the beers quality manufactured by the same producer but bottled in different type of packaging like glass, dose, or PET was made; our results show that no compositional differences among the same beer type exist.