bluuebunny/crossref_metadata_2025 huggingface dataset:
Protection of extreme ultraviolet lithography masks. II. Showerhead flow mitigation of nanoscale particulate contamination
Authors: Klebanoff Leonard E. , Torczynski John R. , Geller Anthony S. , Gallis Michael A. , Rader Daniel J. , Chilese Frank C. , Garcia Rudy F. , Delgado Gil
Published: March 2015

An analysis is presented of a method to protect the reticle (mask) in an extreme ultraviolet (EUV) mask inspection tool using a showerhead plenum to provide a continuous flow of clean gas over the surface of a reticle. The reticle is suspended in an inverted fashion (face down) within a stage/holder that moves back and forth over the showerhead plenum as the reticle is inspected. It is essential that no particles of 10-nm diameter or larger be deposited on the reticle during inspection. Particles can originate from multiple sources in the system, and mask protection from each source is explicitly analyzed. The showerhead plate has an internal plenum with a solid conical wall isolating the aperture. The upper and lower surfaces of the plate are thin flat sheets of porous-metal material. These porous sheets form the top and bottom showerheads that supply the region between the showerhead plate and the reticle and the region between the conical aperture and the Optics Zone box with continuous flows of clean gas. The model studies show that the top showerhead provides robust reticle protection from particles of 10-nm diameter or larger originating from the Reticle Zone and from plenum surfaces contaminated by exposure to the Reticle Zone. Protection is achieved with negligible effect on EUV transmission. The bottom showerhead efficiently protects the reticle from nanoscale particles originating from the Optics Zone. With similar mass flow rates from the two showerheads, this system provides efficient protection even when a significant overpressure exists between the Optics Zone and the Reticle Zone. Performance is insensitive to the fraction of incident particles that sticks to walls, the accommodation coefficient, the aperture geometry, and the gas pressure. The showerheads also protect the aperture (and therefore the Optics Zone) during mask loading and unloading. Commercially available porous-metal media have properties suitable for these showerheads at the required flow rates. The benefits of the approach compared to a conceptual EUV pellicle are described.
Fiber‐optic detector for real time dosimetry of a micro‐planar x‐ray beam
Authors: Belley Matthew D. , Stanton Ian N. , Hadsell Mike , Ger Rachel , Langloss Brian W. , Lu Jianping , Zhou Otto , Chang Sha X. , Therien Michael J. , Yoshizumi Terry T.
Published: March 2015

Purpose:

Here, the authors describe a dosimetry measurement technique for microbeam radiation therapy using a nanoparticle‐terminated fiber‐optic dosimeter (nano‐FOD).

Methods:

The nano‐FOD was placed in the center of a 2 cm diameter mouse phantom to measure the deep tissue dose and lateral beam profile of a planar x‐ray microbeam.

Results:

The continuous dose rate at the x‐ray microbeam peak measured with the nano‐FOD was 1.91 ± 0.06 cGy s−1, a value 2.7% higher than that determined via radiochromic film measurements (1.86 ± 0.15 cGy s−1). The nano‐FOD‐determined lateral beam full‐width half max value of 420 μm exceeded that measured using radiochromic film (320 μm). Due to the 8° angle of the collimated microbeam and resulting volumetric effects within the scintillator, the profile measurements reported here are estimated to achieve a resolution of ∼0.1 mm; however, for a beam angle of 0°, the theoretical resolution would approach the thickness of the scintillator (∼0.01 mm).

Conclusions:

This work provides proof‐of‐concept data and demonstrates that the novel nano‐FOD device can be used to perform real‐time dosimetry in microbeam radiation therapy to measure the continuous dose rate at the x‐ray microbeam peak as well as the lateral beam shape.
Evolution of spatial resolution in breast CT at UC Davis
Authors: Gazi Peymon M. , Yang Kai , Burkett George W. , Aminololama‐Shakeri Shadi , Anthony Seibert J. , Boone John M.
Published: March 2015

Purpose:

Dedicated breast computed tomography (bCT) technology for the purpose of breast cancer screening has been a focus of research at UC Davis since the late 1990s. Previous studies have shown that improvement in spatial resolution characteristics of this modality correlates with greater microcalcification detection, a factor considered a potential limitation of bCT. The aim of this study is to improve spatial resolution as characterized by the modulation transfer function (MTF) via changes in the scanner hardware components and operational schema.

Methods:

Four prototypes of pendant‐geometry, cone‐beam breast CT scanners were designed and developed spanning three generations of design evolution. To improve the system MTF in each bCT generation, modifications were made to the imaging components (x‐ray tube and flat‐panel detector), system geometry (source‐to‐isocenter and detector distance), and image acquisition parameters (technique factors, number of projections, system synchronization scheme, and gantry rotational speed).

Results:

Characterization of different generations of bCT systems shows these modifications resulted in a 188% improvement of the limiting MTF properties from the first to second generation and an additional 110% from the second to third. The intrinsic resolution degradation in the azimuthal direction observed in the first generation was corrected by changing the acquisition from continuous to pulsed x‐ray acquisition. Utilizing a high resolution detector in the third generation, along with modifications made in system geometry and scan protocol, resulted in a 125% improvement in limiting resolution. An additional 39% improvement was obtained by changing the detector binning mode from 2 × 2 to 1 × 1.

Conclusions:

These results underscore the advancement in spatial resolution characteristics of breast CT technology. The combined use of a pulsed x‐ray system, higher resolution flat‐panel detector and changing the scanner geometry and image acquisition logic resulted in a significant fourfold improvement in MTF.
Vocal learning in a social mammal: Demonstrated by isolation and playback experiments in bats
Authors: Prat Yosef , Taub Mor , Yovel Yossi
Published: March 2015

Isolation and playback experiments demonstrate vocal learning in bats and reveal the learning mechanism by continuous recordings from birth.
A general route to nanocrystal kebabs periodically assembled on stretched flexible polymer shish
Authors: Xu Hui , Xu Yuci , Pang Xinchang , He Yanjie , Jung Jaehan , Xia Haiping , Lin Zhiqun
Published: March 2015

Organic-inorganic 1D periodic necklace-like nanostructures are fabricated using confined synthesis of inorganic nanocrystals.
Identification of Anthraquinone-Degrading Bacteria in Soil Contaminated with Polycyclic Aromatic Hydrocarbons
Authors: Rodgers-Vieira Elyse A. , Zhang Zhenfa , Adrion Alden C. , Gold Avram , Aitken Michael D.
Published: March 2015

Quinones and other oxygenated polycyclic aromatic hydrocarbons (oxy-PAHs) are toxic and/or genotoxic compounds observed to be cocontaminants at PAH-contaminated sites, but their formation and fate in contaminated environmental systems have not been well studied. Anthracene-9,10-dione (anthraquinone) has been found in most PAH-contaminated soils and sediments that have been analyzed for oxy-PAHs. However, little is known about the biodegradation of oxy-PAHs, and no bacterial isolates have been described that are capable of growing on or degrading anthraquinone. PAH-degrading
Mycobacterium
spp. are the only organisms that have been investigated to date for metabolism of a PAH quinone, 4,5-pyrenequinone. We utilized DNA-based stable-isotope probing (SIP) with [U-
13
C]anthraquinone to identify bacteria associated with anthraquinone degradation in PAH-contaminated soil from a former manufactured-gas plant site both before and after treatment in a laboratory-scale bioreactor. SIP with [U-
13
C]anthracene was also performed to assess whether bacteria capable of growing on anthracene are the same as those identified to grow on anthraquinone. Organisms closely related to
Sphingomonas
were the most predominant among the organisms associated with anthraquinone degradation in bioreactor-treated soil, while organisms in the genus
Phenylobacterium
comprised the majority of anthraquinone degraders in the untreated soil. Bacteria associated with anthracene degradation differed from those responsible for anthraquinone degradation. These results suggest that
Sphingomonas
and
Phenylobacterium
species are associated with anthraquinone degradation and that anthracene-degrading organisms may not possess mechanisms to grow on anthraquinone.
A MarR Family Transcriptional Regulator, DptR3, Activates Daptomycin Biosynthesis and Morphological Differentiation in Streptomyces roseosporus
Authors: Zhang Qinling , Chen Qiong , Zhuang Shuai , Chen Zhi , Wen Ying , Li Jilun
Published: March 2015

Daptomycin produced by
Streptomyces roseosporus
is an important lipopeptide antibiotic used to treat human infections caused by Gram-positive pathogenic bacteria, including drug-resistant strains. The genetic basis for regulatory mechanisms of daptomycin production is poorly known. Here, we characterized the
dptR3
gene, which encodes a MarR family transcriptional regulator located adjacent to the known daptomycin biosynthetic (
dpt
) genes. Deletion of
dptR3
reduced daptomycin production significantly and delayed aerial mycelium formation and sporulation on solid media. Dissection of the mechanism underlying the function of DptR3 in daptomycin production revealed that it stimulates daptomycin production indirectly by altering the transcription of
dpt
structural genes. DptR3 directly activated the transcription of its own gene,
dptR3
, but repressed the transcription of the adjacent, divergent gene
orf16
(which encodes a putative ABC transporter ATP-binding protein). A 66-nucleotide DptR3-binding site in the intergenic region of
dptR3-orf16
was determined by DNase I footprinting, and the palindromic sequence
TCATTGT
TACCTATGCTC
ACAATGA
(underlining indicates inverted repeats) in the protected region was found to be essential for DptR3 binding.
orf16
, the major target gene of DptR3, exerted a positive effect on daptomycin biosynthesis. Our findings indicate that DptR3 functions as a global regulator that positively controls daptomycin production and morphological development in
S. roseosporus
.
Diversity of Shiga Toxin-Producing Escherichia coli (STEC) O26:H11 Strains Examined via
stx
Subtypes and Insertion Sites of Stx and EspK Bacteriophages
Authors: Bonanno Ludivine , Loukiadis Estelle , Mariani-Kurkdjian Patricia , Oswald Eric , Garnier Lucille , Michel Valérie , Auvray Frédéric
Published: March 2015

Shiga toxin-producing
Escherichia coli
(STEC) is a food-borne pathogen that may be responsible for severe human infections. Only a limited number of serotypes, including O26:H11, are involved in the majority of serious cases and outbreaks. The main virulence factors, Shiga toxins (Stx), are encoded by bacteriophages. Seventy-four STEC O26:H11 strains of various origins (including human, dairy, and cattle) were characterized for their
stx
subtypes and Stx phage chromosomal insertion sites. The majority of food and cattle strains possessed the
stx
1a
subtype, while human strains carried mainly
stx
1a
or
stx
2a
. The
wrbA
and
yehV
genes were the main Stx phage insertion sites in STEC O26:H11, followed distantly by
yecE
and
sbcB
. Interestingly, the occurrence of Stx phages inserted in the
yecE
gene was low in dairy strains. In most of the 29
stx
-negative
E. coli
O26:H11 strains also studied here, these bacterial insertion sites were vacant. Multilocus sequence typing of 20
stx
-positive or
stx
-negative
E. coli
O26:H11 strains showed that they were distributed into two phylogenetic groups defined by sequence type 21 (ST21) and ST29. Finally, an EspK-carrying phage was found inserted in the
ssrA
gene in the majority of the STEC O26:H11 strains but in only a minority of the
stx
-negative
E. coli
O26:H11 strains. The differences in the
stx
subtypes and Stx phage insertion sites observed in STEC O26:H11 according to their origin might reflect that strains circulating in cattle and foods are clonally distinct from those isolated from human patients.
An
l
-Fucose Operon in the Probiotic Lactobacillus rhamnosus GG Is Involved in Adaptation to Gastrointestinal Conditions
Authors: Becerra Jimmy E. , Yebra María J. , Monedero Vicente
Published: March 2015

l
-Fucose is a sugar present in human secretions as part of human milk oligosaccharides, mucins, and other glycoconjugates in the intestinal epithelium. The genome of the probiotic
Lactobacillus rhamnosus
GG (LGG) carries a gene cluster encoding a putative
l
-fucose permease (
fucP
),
l
-fucose catabolic pathway (
fucI
,
fucK
,
fucU
, and
fucA
), and a transcriptional regulator (
fucR
). The metabolism of
l
-fucose in LGG results in 1,2-propanediol production, and their
fucI
and
fucP
mutants displayed a severe and mild growth defect on
l
-fucose, respectively. Transcriptional analysis revealed that the
fuc
genes are induced by
l
-fucose and subject to a strong carbon catabolite repression effect. This induction was triggered by FucR, which acted as a transcriptional activator necessary for growth on
l
-fucose. LGG utilized fucosyl-α1,3-
N
-acetylglucosamine and contrarily to other lactobacilli, the presence of
fuc
genes allowed this strain to use the
l
-fucose moiety. In
fucI
and
fucR
mutants, but not in
fucP
mutant,
l
-fucose was not metabolized and it was excreted to the medium during growth on fucosyl-α1,3-
N
-acetylglucosamine. The
fuc
genes were induced by this fucosyl-disaccharide in the wild type and the
fucP
mutant but not in a
fucI
mutant, showing that FucP does not participate in the regulation of
fuc
genes and that
l
-fucose metabolism is needed for FucR activation. The
l
-fucose operon characterized here constitutes a new example of the many factors found in LGG that allow this strain to adapt to the gastrointestinal conditions.
Latex Clearing Protein (Lcp) of Streptomyces sp. Strain K30 Is a
b
-Type Cytochrome and Differs from Rubber Oxygenase A (RoxA) in Its Biophysical Properties
Authors: Birke Jakob , Röther Wolf , Jendrossek Dieter
Published: March 2015

Specific polyisoprene-cleaving activities of 1.5 U/mg and 4.6 U/mg were determined for purified Strep-tagged latex clearing protein (Lcp) of
Streptomyces
sp. strain K30 at 23°C and 37°C, respectively. Metal analysis revealed the presence of approximately one atom of iron per Lcp molecule. Copper, which had been identified in Lcp1
VH2
of
Gordonia polyisoprenivorans
previously, was below the detection limit in Lcp
K30
. Heme was identified as a cofactor in purified Lcp
K30
by (i) detection of characteristic α-, β-, and γ (Soret)-bands at 562 nm, 532 nm, and 430 nm in the visible spectrum after chemical reduction, (ii) detection of an acetone-extractable porphyrin molecule, (iii) determination of a heme
b
-type-specific absorption maximum (556 nm) after chemical conversion of the heme group to a bipyridyl-heme complex, and (iv) detection of a
b
-heme-specific
m/z
value of 616.2 via mass spectrometry. Spectroscopic analysis showed that purified Lcp as isolated contains an oxidized heme-Fe
3+
that is free of bound dioxygen. This is in contrast to the rubber oxygenase RoxA, a
c
-type heme-containing polyisoprene-cleaving enzyme present in Gram-negative rubber degraders, in which the covalently bound heme firmly binds a dioxygen molecule. Lcp
K30
also differed from RoxA in the lengths of the rubber degradation cleavage products and in having a higher melting point of 61.5°C (RoxA, 54.3°C). In summary, RoxA and Lcp both are equipped with a heme cofactor and catalyze an oxidative C-C cleavage reaction but differ in the heme subgroup type and in several biochemical and biophysical properties. These findings suggest differences in the catalytic reaction mechanisms.
Comparison of the Prevalences and Diversities of Listeria Species and Listeria monocytogenes in an Urban and a Rural Agricultural Watershed
Authors: Stea Emma C. , Purdue Laura M. , Jamieson Rob C. , Yost Chris K. , Truelstrup Hansen Lisbeth
Published: March 2015

Foods and related processing environments are commonly contaminated with the pathogenic
Listeria monocytogenes
. To investigate potential environmental reservoirs of
Listeria
spp. and
L. monocytogenes
, surface water and point source pollution samples from an urban and a rural municipal water supply watershed in Nova Scotia, Canada, were examined over 18 months. Presumptive
Listeria
spp. were cultured from 72 and 35% of rural and urban water samples, respectively, with 24% of the positive samples containing two or three different
Listeria
spp. The
L. innocua
(56%) and
L. welshimeri
(43%) groups were predominant in the rural and urban watersheds, respectively. Analysis by the TaqMan assay showed a significantly (
P
< 0.05) higher prevalence of
L. monocytogenes
of 62% versus 17% by the culture-based method. Both methods revealed higher prevalences in the rural watershed and during the fall and winter seasons. Elevated
Escherichia coli
(≥100 CFU/100 ml) levels were not associated with the pathogen regardless of the detection method. Isolation of
Listeria
spp. were associated with 70 times higher odds of isolating
L. monocytogenes
(odds ratio = 70;
P
< 0.001). Serogroup IIa was predominant (67.7%) among the 285
L. monocytogenes
isolates, followed by IVb (16.1%), IIb (15.8%), and IIc (0.4%).
L. monocytogenes
was detected in cow feces and raw sewage but not in septic tank samples. Pulsotyping of representative water (
n
= 54) and local human (
n
= 19) isolates suggested genetic similarities among some environmental and human
L. monocytogenes
isolates. In conclusion, temperate surface waters contain a diverse
Listeria
species population and could be a potential reservoir for
L. monocytogenes
, especially in rural agricultural watersheds.
Mutational Analysis of the Antitoxin in the Lactococcal Type III Toxin-Antitoxin System AbiQ
Authors: Bélanger Maxime , Moineau Sylvain
Published: March 2015

The lactococcal abortive phage infection mechanism AbiQ recently was classified as a type III toxin-antitoxin system in which the toxic protein (ABIQ) is regulated following cleavage of its repeated noncoding RNA antitoxin (
antiQ
). In this study, we investigated the role of the antitoxin in antiphage activity. The cleavage of
antiQ
by ABIQ was characterized using 5′ rapid amplification of cDNA ends PCR and was located in an adenine-rich region of
antiQ
. We next generated a series of derivatives with point mutations within
antiQ
or with various numbers of
antiQ
repetitions. These modifications were analyzed for their effect on the antiphage activity (efficiency of plaquing) and on the endoribonuclease activity (Northern hybridization). We observed that increasing or reducing the number of
antiQ
repeats significantly decreased the antiphage activity of the system. Several point mutations had a similar effect on the antiphage activity and were associated with changes in the digestion profile of
antiQ
. Interestingly, a point mutation in the putative pseudoknot structure of
antiQ
mutants led to an increased AbiQ antiphage activity, thereby offering a novel way to increase the activity of an abortive infection mechanism.
Infection Density Dynamics of the Citrus Greening Bacterium “Candidatus Liberibacter asiaticus” in Field Populations of the Psyllid Diaphorina citri and Its Relevance to the Efficiency of Pathogen Transmission to Citrus Plants
Authors: Ukuda-Hosokawa Rie , Sadoyama Yasutsune , Kishaba Misaki , Kuriwada Takashi , Anbutsu Hisashi , Fukatsu Takema
Published: March 2015

Huanglongbing, or citrus greening, is a devastating disease of citrus plants recently spreading worldwide, which is caused by an uncultivable bacterial pathogen, “
Candidatus
Liberibacter asiaticus,” and vectored by a phloem-sucking insect,
Diaphorina citri
. We investigated the infection density dynamics of “
Ca
. Liberibacter asiaticus” in field populations of
D. citri
with experiments using field-collected insects to address how “
Ca
. Liberibacter asiaticus” infection density in the vector insect is relevant to pathogen transmission to citrus plants. Of 500 insects continuously collected from “
Ca
. Liberibacter asiaticus”-infected citrus trees with pathological symptoms in the spring and autumn of 2009, 497 (99.4%) were “
Ca
. Liberibacter asiaticus” positive. The infections were systemic across head-thorax and abdomen, ranging from 10
3
to 10
7
bacteria per insect. In spring, the infection densities were low in March, at ∼10
3
bacteria per insect, increasing up to 10
6
to 10
7
bacteria per insect in April and May, and decreasing to 10
5
to 10
6
bacteria per insect in late May, whereas the infection densities were constantly ∼10
6
to 10
7
bacteria per insect in autumn. Statistical analysis suggested that several factors, such as insect sex, host trees, and collection dates, may be correlated with “
Ca
. Liberibacter asiaticus” infection densities in field
D. citri
populations. Inoculation experiments with citrus seedlings using field-collected “
Ca
. Liberibacter asiaticus”-infected insects suggested that (i) “
Ca
. Liberibacter asiaticus”-transmitting insects tend to exhibit higher infection densities than do nontransmitting insects, (ii) a threshold level (∼10
6
bacteria per insect) of “
Ca
. Liberibacter asiaticus” density in
D. citri
is required for successful transmission to citrus plants, and (iii)
D. citri
attaining the threshold infection level transmits “
Ca
. Liberibacter asiaticus” to citrus plants in a stochastic manner. These findings provide valuable insights into understanding, predicting, and controlling this notorious citrus pathogen.
Electrical Stimulation Improves Microbial Salinity Resistance and Organofluorine Removal in Bioelectrochemical Systems
Authors: Feng Huajun , Zhang Xueqin , Guo Kun , Vaiopoulou Eleni , Shen Dongsheng , Long Yuyang , Yin Jun , Wang Meizhen
Published: March 2015

Fed batch bioelectrochemical systems (BESs) based on electrical stimulation were used to treat
p
-fluoronitrobenzene (
p
-FNB) wastewater at high salinities. At a NaCl concentration of 40 g/liter,
p
-FNB was removed 100% in 96 h in the BES, whereas in the biotic control (BC) (absence of current),
p
-FNB removal was only 10%. By increasing NaCl concentrations from 0 g/liter to 40 g/liter, defluorination efficiency decreased around 40% in the BES, and in the BC it was completely ceased.
p
-FNB was mineralized by 30% in the BES and hardly in the BC. Microorganisms were able to store 3.8 and 0.7 times more K
+
and Na
+
intracellularly in the BES than in the BC. Following the same trend, the ratio of protein to soluble polysaccharide increased from 3.1 to 7.8 as the NaCl increased from 0 to 40 g/liter. Both trends raise speculation that an electrical stimulation drives microbial preference toward K
+
and protein accumulation to tolerate salinity. These findings are in accordance with an enrichment of halophilic organisms in the BES.
Halobacterium
dominated in the BES by 56.8% at a NaCl concentration of 40 g/liter, while its abundance was found as low as 17.5% in the BC. These findings propose a new method of electrical stimulation to improve microbial salinity resistance.
The effect of occupational noise exposure on tinnitus and sound-induced auditory fatigue among obstetrics personnel: a cross-sectional study
Authors: Fredriksson Sofie , Hammar Oscar , Torén Kjell , Tenenbaum Artur , Waye Kerstin Persson
Published: March 2015

Objective

There is a lack of research on effects of occupational noise exposure in traditionally female-dominated workplaces. Therefore, the aim of this study was to assess risk of noise-induced hearing-related symptoms among obstetrics personnel.

Design

A cross-sectional study was performed at an obstetric ward in Sweden including a questionnaire among all employees and sound level measurements in 61 work shifts at the same ward.

Participants

115 female employees responded to a questionnaire (72% of all 160 employees invited).

Main outcome measures

Self-reported hearing-related symptoms in relation to calculated occupational noise exposure dose and measured sound levels.

Results

Sound levels exceeded the 80 dB LAeq limit for protection of hearing in 46% of the measured work shifts. One or more hearing-related symptoms were reported by 55% of the personnel. In logistic regression models, a significant association was found between occupational noise exposure dose and tinnitus (OR=1.04, 95% CI 1.00 to 1.09) and sound-induced auditory fatigue (OR=1.04, 95% CI 1.00 to 1.07). Work-related stress and noise annoyance at work were reported by almost half of the personnel. Sound-induced auditory fatigue was associated with work-related stress and noise annoyance at work, although stress slightly missed significance in a multivariable model. No significant interactions were found.

Conclusions

This study presents new results showing that obstetrics personnel are at risk of noise-induced hearing-related symptoms. Current exposure levels at the workplace are high and occupational noise exposure dose has significant effects on tinnitus and sound-induced auditory fatigue among the personnel. These results indicate that preventative action regarding noise exposure is required in obstetrics care and that risk assessments may be needed in previously unstudied non-industrial communication-intense sound environments.
Polyostotic osteomyelitis following open pyometra in a dog
Authors: Yanai Hadar , Jakovljevic Samuel , Dye Charlotte , Tappin Simon
Published: March 2015

A six‐year‐old female neutered Löwchen with a clinical history of ovariohysterectomy following open pyometra was referred for evaluation of severe progressive generalised lameness in all four limbs, of varying degrees of severity and pyrexia that developed over the two weeks following surgery. Physical examination revealed enlarged superficial cervical lymph nodes, pain on deep palpation of both humeri and a grade I/VI cardiac murmur. Radiographs demonstrated irregular solid periosteal new bone involving the diaphyses of the humeri, femora and several ribs. Serum biochemistry showed mildly decreased urea levels and mildly elevated alkaline phosphatase. Haematology revealed mild thrombocytosis. A preliminary diagnosis of osteomyelitis was made. Biopsies of the bone lesions were taken, and bacteriological cultures with susceptibility testing confirmed a diagnosis of Escherichia coli. Following six weeks of medical treatment with meloxicam, tramadol and marbofloxacin, the clinical signs resolved and follow‐up radiographs obtained 12 weeks from initial presentation supported the resolution of the clinical signs. To the authors’ knowledge, this is the first reported case of haematogenous osteomyelitis presumably spreading from the uterus, involving multiple bones and leading to complete resolution with medical treatment.
A Cooperative Coevolution Approach to Automate Pattern-based Software Architectural Synthesis
Authors: Xu Yongrui , Liang Peng
Published: March 2015

To reuse successful experience in software architecture design, architects use architectural patterns as reusable architectural knowledge for architectural synthesis. However, it has been observed that the resulting architecture does not always conform to the initial architectural patterns employed. Architectural synthesis using architectural patterns is also recognized as a challenging task, especially for novice architects due to lack of experience. In this paper, we propose a cooperative coevolution approach to automate architectural synthesis using architectural patterns. We first analyze several common architectural patterns and the constraints when using them. We then extend existing architectural synthesis activity with patterns based on the results of this analysis. Finally, we map the extended architectural synthesis to a cooperative coevolution model, which can optimize the resulting architectural solutions and avoid the violations to the pattern constraints automatically. We evaluate the proposed approach through a case study: architecture design of a cinema booking system. The results show that the proposed approach can generate architectural solutions which are closer to the expert design.
A geometric Hamiltonian description of composite quantum systems and quantum entanglement
Authors: Pastorello Davide
Published: March 2015

Finite-dimensional Quantum Mechanics can be geometrically formulated as a proper classical-like Hamiltonian theory in a projective Hilbert space. The description of composite quantum systems within the geometric Hamiltonian framework is discussed in this paper. As summarized in the first part of this work, in the Hamiltonian formulation the phase space of a quantum system is the Kähler manifold given by the complex projective space P(H) of the Hilbert space H of the considered quantum theory. However the phase space of a bipartite system must be P(H1 ⊗ H2) and not simply P(H1) × P(H2) as suggested by the analogy with Classical Mechanics. A part of this paper is devoted to manage this problem. In the second part of the work, a definition of quantum entanglement and a proposal of entanglement measure are given in terms of a geometrical point of view (a rather studied topic in recent literature). Finally two known separability criteria are implemented in the Hamiltonian formalism.
Identifying geological materials from nineteenth-century residential and industrial properties in south Glasgow: the M74 excavations
Authors: Hayward K. M. J.
Published: March 2015

The industrial and residential expansion of south Glasgow from the second and third quarters of the nineteenth century onwards, required enormous volumes of dressed stone, paving, setts and bricks for building construction. Most quarries and clay pits dating from this period now lie buried beneath the modern urban Glasgow landscape, cut off from the scant documentary evidence of the quarrying and supply of these materials. Petrological and geochemical studies of the stone and construction bricks recovered from archaeological excavations of the remains of nineteenth-century buildings, carried out in advance of construction of the M74 completion project in Glasgow and south Lanarkshire, provide evidence of the locations from which these materials were extracted. The sites investigated comprise the locations of former industrial and domestic buildings. The results indicate that the raw materials for the bulk of the dressed stone and stock bricks were extracted from quarries and clay pits in underlying Upper Carboniferous strata in the Glasgow area. Four poor quality Upper Carboniferous ‘blonde’ sandstones from early nineteenth-century buildings are similar to variants described previously, but sources have not been identified. Better quality ‘Giffnock’ sandstones, derived from Upper Carboniferous–Upper Limestone Formation (Clackmannan Group) quarries south of Rutherglen and present in later buildings, demonstrate that the quarrying and supply of these sandstones became progressively more centralized, probably due to the expansion of the railway network. A more specialized set of worked stone materials (paving slabs, setts and roofing), recovered from nineteenth-century tenement blocks and a Mill Owner’s House, show that this group was brought in from further afield (Caithness and the West Highlands). Construction bricks have geochemical signatures comparable with those of the underlying Coal Measure mudstones. Analyses of bricks with known brick stamps provide a template with which to compare the geological fingerprints of earlier ‘1830–60’ unstamped stock bricks. Discriminant analysis matches many of these with early local brick manufacturers, although some remain ‘unknown’. The tradition of using local construction materials, first in freestone and then in construction bricks, demonstrates that the economic potential of the underlying Carboniferous strata was fully exploited both in an independent industry and in parallel with coal mining, fireclay and iron-ore extraction.
Coronary vasomotor responses to isometric handgrip exercise are primarily mediated by nitric oxide: a noninvasive MRI test of coronary endothelial function
Authors: Hays Allison G. , Iantorno Micaela , Soleimanifard Sahar , Steinberg Angela , Schär Michael , Gerstenblith Gary , Stuber Matthias , Weiss Robert G.
Published: March 2015

Endothelial cell release of nitric oxide (NO) is a defining characteristic of nondiseased arteries, and abnormal endothelial NO release is both a marker of early atherosclerosis and a predictor of its progression and future events. Healthy coronaries respond to endothelial-dependent stressors with vasodilatation and increased coronary blood flow (CBF), but those with endothelial dysfunction respond with paradoxical vasoconstriction and reduced CBF. Recently, coronary MRI and isometric handgrip exercise (IHE) were reported to noninvasively quantify coronary endothelial function (CEF). However, it is not known whether the coronary response to IHE is actually mediated by NO and/or whether it is reproducible over weeks. To determine the contribution of NO, we studied the coronary response to IHE before and during infusion of NG-monomethyl-l-arginine (l-NMMA, 0.3 mg·kg−1·min−1), a NO-synthase inhibitor, in healthy volunteers. For reproducibility, we performed two MRI-IHE studies ∼8 wk apart in healthy subjects and patients with coronary artery disease (CAD). Changes from rest to IHE in coronary cross-sectional area (%CSA) and diastolic CBF (%CBF) were quantified. l-NMMA completely blocked normal coronary vasodilation during IHE [%CSA, 12.9 ± 2.5 (mean ± SE, placebo) vs. −0.3 ± 1.6% (l-NMMA); P < 0.001] and significantly blunted the increase in flow [%CBF, 47.7 ± 6.4 (placebo) vs. 10.6 ± 4.6% (l-NMMA); P < 0.001]. MRI-IHE measures obtained weeks apart strongly correlated for CSA ( P < 0.0001) and CBF ( P < 0.01). In conclusion, the normal human coronary vasoactive response to IHE is primarily mediated by NO. This noninvasive, reproducible MRI-IHE exam of NO-mediated CEF promises to be useful for studying CAD pathogenesis in low-risk populations and for evaluating translational strategies designed to alter CAD in patients.
Interleukin-6 mediates exercise preconditioning against myocardial ischemia reperfusion injury
Authors: McGinnis Graham Ripley , Ballmann Christopher , Peters Bridget , Nanayakkara Gayani , Roberts Michael , Amin Rajesh , Quindry John C.
Published: March 2015

Interleukin-6 (IL-6) is a pleiotropic cytokine that protects against cardiac ischemia-reperfusion (I/R) injury following pharmacological and ischemic preconditioning (IPC), but the affiliated role in exercise preconditioning is unknown. Our study purpose was to characterize exercise-induced IL-6 cardiac signaling ( aim 1) and evaluate myocardial preconditioning ( aim 2). In aim 1, C57 and IL-6−/− mice underwent 3 days of treadmill exercise for 60 min/day at 18 m/min. Serum, gastrocnemius, and heart were collected preexercise, immediately postxercise, and 30 and 60 min following the final exercise session and analyzed for indexes of IL-6 signaling. For aim 2, a separate cohort of exercise-preconditioned (C57 EX and IL-6−/− EX) and sedentary (C57 SED and IL-6−/− SED) mice received surgical I/R injury (30 min I, 120 min R) or a time-matched sham operation. Ischemic and perfused tissues were examined for necrosis, apoptosis, and autophagy. In aim 1, serum IL-6 and IL-6 receptor (IL-6R), gastrocnemius, and myocardial IL-6R were increased following exercise in C57 mice only. Phosphorylated (p) signal transducer and activator of transcription 3 was increased in gastrocnemius and heart in C57 and IL-6−/− mice postexercise, whereas myocardial iNOS and cyclooxygenase-2 were unchanged in the exercised myocardium. Exercise protected C57 EX mice against I/R-induced arrhythmias and necrosis, whereas arrhythmia score and infarct outcomes were higher in C57 SED, IL-6−/− SED, and IL-6−/− EX mice compared with SH. C57 EX mice expressed increased p-p44/42 MAPK (Thr202/Tyr204) and p-p38 MAPK (Thr180/Tyr182) compared with IL-6−/− EX mice, suggesting pathway involvement in exercise preconditioning. Findings indicate exercise exerts cardioprotection via IL-6 and strongly implicates protective signaling originating from the exercised skeletal muscle.
Attenuating endogenous Fgfr2b ligands during bleomycin-induced lung fibrosis does not compromise murine lung repair
Authors: MacKenzie BreAnne , Henneke Ingrid , Hezel Stefanie , Al Alam Denise , El Agha Elie , Chao Cho-Ming , Quantius Jennifer , Wilhelm Jochen , Jones Matthew , Goth Kerstin , Li Xiaokun , Seeger Werner , Königshoff Melanie , Herold Susanne , Rizvanov Albert A. , Günther Andreas , Bellusci Saverio
Published: March 2015

Fibroblast growth factors (Fgfs) mediate organ repair. Lung epithelial cell overexpression of Fgf10 postbleomycin injury is both protective and therapeutic, characterized by increased survival and attenuated fibrosis. Exogenous administration of FGF7 (palifermin) also showed prophylactic survival benefits in mice. The role of endogenous Fgfr2b ligands on bleomycin-induced lung fibrosis is still elusive. This study reports the expression of endogenous Fgfr2b ligands, receptors, and signaling targets in wild-type mice following bleomycin lung injury. In addition, the impact of attenuating endogenous Fgfr2b-ligands following bleomycin-induced fibrosis was tested by using a doxycycline (dox)-based inducible, soluble, dominant-negative form of the Fgfr2b receptor. Double-transgenic (DTG) Rosa26rtTA/+;tet(O)solFgfr2b mice were validated for the expression and activity of soluble Fgfr2b (failure to regenerate maxillary incisors, attenuated recombinant FGF7 signal in the lung). As previously reported, no defects in lung morphometry were detected in DTG (+dox) mice exposed from postnatal days (PN) 1 through PN105. Female single-transgenic (STG) and DTG mice were subjected to various levels of bleomycin injury (1.0, 2.0, and 3.0 U/kg). Fgfr2b ligands were attenuated either throughout injury ( days 0– 11; days 0– 28) or during later stages ( days 6– 28 and 14– 28). No significant changes in survival, weight, lung function, confluent areas of fibrosis, or hydroxyproline deposition were detected in DTG mice. These results indicate that endogenous Fgfr2b ligands do not significantly protect against bleomycin injury, nor do they expedite the resolution of bleomycin-induced lung injury in mice.
Evaluation and Application of the Strand-Specific Protocol for Next-Generation Sequencing
Authors: Tsai Kuo-Wang , Chang Bill , Pan Cheng-Tsung , Lin Wei-Chen , Chen Ting-Wen , Li Sung-Chou
Published: March 2015

Next-generation sequencing (NGS) has become a powerful sequencing tool, applied in a wide range of biological studies. However, the traditional sample preparation protocol for NGS is non-strand-specific (NSS), leading to biased estimates of expression for transcripts overlapped at the antisense strand. Strand-specific (SS) protocols have recently been developed. In this study, we prepared the same RNA sample by using the SS and NSS protocols, followed by sequencing with Illumina HiSeq platform. Using real-time quantitative PCR as a standard, we first proved that the SS protocol more precisely estimates gene expressions compared with the NSS protocol, particularly for those overlapped at the antisense strand. In addition, we also showed that the sequence reads from the SS protocol are comparable with those from conventional NSS protocols in many aspects. Finally, we also mapped a fraction of sequence reads back to the antisense strand of the known genes, originally without annotated genes located. Using sequence assembly and PCR validation, we succeeded in identifying and characterizing the novel antisense genes. Our results show that the SS protocol performs more accurately than the traditional NSS protocol and can be applied in future studies.
A New Recommendation Algorithm Based on User’s Dynamic Information in Complex Social Network
Authors: Cheng Jiujun , Liu Yingbo , Zhang Huiting , Wu Xiao , Chen Fuzhen
Published: March 2015

The development of recommendation system comes with the research of data sparsity, cold start, scalability, and privacy protection problems. Even though many papers proposed different improved recommendation algorithms to solve those problems, there is still plenty of room for improvement. In the complex social network, we can take full advantage of dynamic information such as user’s hobby, social relationship, and historical log to improve the performance of recommendation system. In this paper, we proposed a new recommendation algorithm which is based on social user’s dynamic information to solve the cold start problem of traditional collaborative filtering algorithm and also considered the dynamic factors. The algorithm takes user’s response information, dynamic interest, and the classic similar measurement of collaborative filtering algorithm into account. Then, we compared the new proposed recommendation algorithm with the traditional user based collaborative filtering algorithm and also presented some of the findings from experiment. The results of experiment demonstrate that the new proposed algorithm has a better recommended performance than the collaborative filtering algorithm in cold start scenario.
Pharmacological Basis for Traditional Use of theLippia thymoides
Authors: Silva Fabrício Souza , Menezes Pedro Modesto Nascimento , Sá Pedro Guilherme Souza de , Oliveira André Luís de Santana , Souza Eric Alencar Araújo , Bamberg Vinicius Martins , de Oliveira Henrique Ribeiro , Oliveira Sheilla Andrade de , Araújo Roni Evêncio e , Uetanabaro Ana Paula Trovatti , Silva Tânia Regina dos Santos , Almeida Jackson Roberto Guedes da Silva , Lucchese Angélica Maria
Published: March 2015

The aim of this study was to evaluate crude extracts and fractions from leaves and stems ofLippia thymoidesand to validate their use in folk medicine.In vitroantioxidant and antimicrobial activities andin vivowound healing in rats, baker yeast-induced fever in young rats, and acute oral toxicity in mice assays were realized. The crude extracts and their dichloromethane and ethyl acetate fractions had potent radical-scavenging activity against the DPPH but were not effective in theβ-carotene bleaching method. The dichloromethane fraction from the leaves extract showed the broadest spectrum of activity againstS. aureus,B. cereus, andC. parapsilosis. The animals treated with crude extracts showed no difference in wound healing when compared with the negative control group. The crude extract from leaves (1200 mg/kg) has equal efficacy in reducing temperature in rats with hyperpyrexia compared to dipyrone (240 mg/kg) and is better than paracetamol (150 mg/kg). In acute toxicity test, crude extract of leaves fromLippia thymoidesexhibited no mortality and behavioral changes and no adverse effects in male and female mice. This work validates the popular use ofLippia thymoidesfor treating the wound and fever, providing a source for biologically active substances.
Care and Neurorehabilitation in the Disorder of Consciousness: A Model in Progress
Authors: Dolce Giuliano , Arcuri Francesco , Carozzo Simone , Cortese Maria Daniela , Greco Pierpaolo , Lucca Lucia Francesca , Pignolo Loris , Pugliese Maria Elena , Riganello Francesco
Published: March 2015

The operational model and strategies developed at the Institute S. Anna‐RAN to be applied in the care and neurorehabilitation of subjects with disorders of consciousness (DOC) are described. The institute units are sequentially organized to guarantee appropriate care and provide rehabilitation programs adapted to the patients’ clinical condition and individual’s needs at each phase of evolution during treatment in a fast turnover rate. Patients eligible of home care are monitored remotely. Transferring advanced technology to a stage of regular operation is the main mission. Responsiveness and the time windows characterized by better residual responsiveness are identified and the spontaneous/induced changes in the autonomic system functional state and biological parameters are monitored both in dedicated sessions and by means of an ambient intelligence platform acquiring large databases from traditional and innovative sensors and interfaced with knowledge management and knowledge discovery systems. Diagnosis of vegetative state/unresponsive wakefulness syndrome or minimal conscious state and early prognosis are in accordance with the current criteria. Over one thousand patients with DOC have been admitted and treated in the years 1998–2013. The model application has progressively shortened the time of hospitalization and reduced costs at unchanged quality of services.
Traceability of PDO Olive Oil “Terra di Bari” Using High Resolution Melting
Authors: Montemurro Cinzia , Miazzi Monica Marilena , Pasqualone Antonella , Fanelli Valentina , Sabetta Wilma , di Rienzo Valentina
Published: March 2015

The aim of the research was to verify the applicability of microsatellite (SSR) markers in High Resolution Melting (HRM) analysis for the identification of the olive cultivars used in the “Terra di Bari” PDO extra virgin olive oil. A panel of nine cultivars, widespread in Apulia region, was tested with seventeen SSR primer pairs and the PCR products were at first analysed with a Genetic Analyzer automatic sequencer. An identification key was obtained for the nine cultivars, which showed an unambiguous discrimination among the varieties constituting the “Terra di Bari” PDO extra virgin olive oil: Cima di Bitonto, Coratina, and Ogliarola. Subsequently, an SSR based method was set up with the DCA18 marker, coupled with HRM analysis for the distinction of the Terra di Bari olive oil from non-Terra di Bari olive oil using different mixtures. Thus, this analysis enabled the distinction and identification of the PDO mixtures. Hence, this assay provided a flexible, cost-effective, and closed-tube microsatellite genotyping method, well suited to varietal identification and authentication analysis in olive oil.
Type I Saikosaponins A and D Inhibit Osteoclastogenesis in Bone Marrow-Derived Macrophages and Osteolytic Activity of Metastatic Breast Cancer Cells
Authors: Shin Ji-Eun , Kim Hyun-Jeong , Kim Ki-Rim , Lee Sun Kyoung , Park Junhee , Kim Hyungkeun , Park Kwang-Kyun , Chung Won-Yoon
Published: March 2015

Many osteopenic disorders, including a postmenopausal osteoporosis and lytic bone metastasis in breast and prostate cancers, are linked with a hyperosteoclast activity due to increased receptor activator of nuclear factor kappa-B ligand (RANKL) expression in osteoblastic/stromal cells. Therefore, inhibition of RANKL-induced osteoclastogenesis and osteoclast-induced bone resorption is an important approach in controlling pathophysiology of these skeletal diseases. We found that, of seven type I, II, and III saikosaponins isolated fromBupleurum falcatum, saikosaponins A and D, type I saikosaponins with an allyl oxide linkage between position 13 and 28 and two carbohydrate chains that are directly attached to the hydroxyl groups in position 3, exhibited the most potent inhibition on RANKL-induced osteoclast formation at noncytotoxic concentrations. The stereochemistry of the hydroxyl group at C16 did not affect their activity. Saikosaponins A and D inhibited the formation of resorptive pits by reducing the secreted levels of matrix metalloproteinase- (MMP-) 2, MMP-9, and cathepsin K in RANKL-induced osteoclasts. Additionally, saikosaponins A and D inhibited mRNA expression of parathyroid hormone-related protein as well as cell viability and invasion in metastatic human breast cancer cells. Thus, saikosaponins A and D can serve as a beneficial agent for the prevention and treatment of osteoporosis and cancer-induced bone loss.