bluuebunny/crossref_metadata_2025_split huggingface dataset:
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.
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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ABSTRACT

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

ObjectiveThere 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.DesignA 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.Participants115 female employees responded to a questionnaire (72% of all 160 employees invited).Main outcome measuresSelf-reported hearing-related symptoms in relation to calculated occupational noise exposure dose and measured sound levels.ResultsSound 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.ConclusionsThis 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.