bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluation of reward from pain relief
Authors: Navratilova Edita , Xie Jennifer Yanhua , King Tamara , Porreca Frank
Published: March 2013

The human experience of pain is multidimensional and comprises sensory, affective, and cognitive dimensions. Preclinical assessment of pain has been largely focused on the sensory features that contribute to nociception. The affective (aversive) qualities of pain are clinically significant but have received relatively less mechanistic investigation in preclinical models. Recently, operant behaviors such as conditioned place preference, avoidance, escape from noxious stimulus, and analgesic drug self‐administration have been used in rodents to evaluate affective aspects of pain. An important advance of such operant behaviors is that these approaches may allow the detection and mechanistic investigation of spontaneous neuropathic or ongoing inflammatory/nociceptive (i.e., nonevoked) pain that is otherwise difficult to assess in nonverbal animals. Operant measures may allow the identification of mechanisms that contribute differentially to reflexive hypersensitivity or to pain affect and may inform the decision to progress novel mechanisms to clinical trials for pain therapy. Additionally, operant behaviors may allow investigation of the poorly understood mechanisms and neural circuits underlying motivational aspects of pain and the reward of pain relief.
Relationship between fixation stability measured with MP‐1 and reading performance
Authors: Amore Filippo M , Fasciani Romina , Silvestri Valeria , Crossland Michael D , de Waure Chiara , Cruciani Filippo , Reibaldi Alfredo
Published: March 2013

Background

People with visual impairment have reduced reading performance, which is thought to be related to unstable or eccentric fixation. New microperimeters such as the MP‐1 offer straightforward analysis of fixation stability. The aim of this study was to investigate the relationship between fixation stability and reading speed in a large cohort of people with diverse causes of visual impairment and to verify the correlation between reading speed and different methods for the quantification of fixation.

Methods

The better eye of one hundred and twenty subjects was assessed. Fixation values were obtained from the MP‐1 microperimeter. Reading speed was evaluated using newspaper text with magnifiers if required.

Results

The poorest fixation stability and reading performance was found in people with age‐related macular degeneration while the best fixation was in retinitis pigmentosa subjects. A linear relationship was found between reading speed and the proportion of fixations within 2° (r² = 0.51, p < 0.001) and 4° (r² = 0.36, p < 0.001). A negative correlation was found between reading speed and all three bivariate contour ellipse areas (BCEA; for log transformation of 1‐S.D., 2‐S.D. and 3‐S.D.: r² = 0.39, p < 0.001). In a multiple regression model, proportion of points falling within 2° and 4° circle was significantly related to reading speed (r² = 0.55, p < 0.01; r² = 0.43 p < 0.01); also BCEAs values were strongly related to reading ability only in patients with central vision loss (r² = 0.62, p < 0.01 for LogBCEA 68.2%; r² = 0.61, p < 0.01 for LogBCEA 95.4% and 99.6%) and peripheral defect (r² = 0.52, p < 0.01 for LogBCEA 68.2%; r² = 0.50, p < 0.01 for LogBCEA 95.4%; r² = 0.49, p < 0.01 for LogBCEA 99.6%) but not in combined defect subjects.

Conclusions

The study confirms that in people with visual impairment the reduced reading performance is correlated with fixation instability. Moreover, there is a strong relationship between reading speed and both the proportion of fixations falling within 2° and 4° and bivariate contour ellipse area values.
“Too gruesome to be fully taken in”: Konstantin Simonov's “The Extermination Camp” as Holocaust Literature
Authors: HICKS JEREMY
Published: March 2013

Konstantin Simonov's article about Majdanek, entitled “The Extermination Camp” and published in Krasnaia zvezda on August 10, 11, and 12, 1944, has typically been dismissed as irrelevant to our understanding of the Holocaust, due to its downplaying of the extent of Jewish victims. However, a detailed analysis of Simonov's article shows it to constitute not only the first but also a worthwhile attempt to grasp the unprecedented and unthinkable nature of the camps. It does so by consciously insisting on the position of the journalist as an immediate eyewitness, rather than as an ideologically authoritative interpreter, as was the Soviet norm. This enables Simonov to attempt to conceptualize the distinct nature of the extermination camp, as opposed to the concentration camp, to describe the gas chambers, intimating the experience of the victims, and to treat the enormous piles of footwear as a form of silent testimony as to the identity and number of the dead. In each case these are errors, but largely understandable and a function of the article's merits as a significant step in the process by which humanity first confronted the inconceivable reality of the Holocaust. In common with most wartime Soviet representations of what we have come to know as the Holocaust, Simonov's “Extermination Camp” is marred by a failure to convey the distinct nature and scale of Jewish victimhood, so that a deeper knowledge of this report enables a firmer sense of the still greater achievement of Vasilii Grossman's The Hell of Treblinka.
Professional education to meet the oral health needs of older adults and persons with disabilities
Authors: Dolan Teresa A.
Published: March 2013

A well‐prepared dental workforce is critical to improving the oral health of special needs patients. This paper, originally presented at the National Coalition Consensus Conference: Oral Health of Vulnerable Older Adults and Persons with Disabilities, reviews and suggests opportunities to enhance the professional education of the dental workforce, including enhanced faculty training in gerontology, geriatrics and special patient care, and opportunities for improved curricula and team training both within the dental team and among the diverse group of health professional that often collaborate in the care of special needs patients. Other considerations include the creation of a specialty of Special Care Dentistry, and the effective use of dental team members in the care of special needs patients.
Structure and hydraulic properties of the boreal clay soil under differently managed buffer zones
Authors: Rasa K. , Horn R.
Published: March 2013

Vegetated buffer zones (BZs) between arable fields and bodies of water are commonly established to reduce erosion and run‐off of particle‐bound nutrients. Functioning of a BZ depends on soil structure, as it is important for water infiltration. Therefore, it is vital to understand how varying management practices affect soils of BZs. We studied the structural and hydraulic properties of three differently managed BZs established in a boreal Vertic Stagnic Cambisol (clay, 51%). The three management practices for vegetation were as follows: natural with no treatment, harvested yearly and grazed by cattle. We used bulk density and macroporosity, together with a pore geometry index (air permeability per unit air‐filled porosity), to describe the soil structural properties. Hydraulic properties were measured at different length scales by means of an aggregate sorptivity test, saturated hydraulic conductivity of the core samples and field‐saturated hydraulic conductivity. Vegetation management markedly affected the physical properties in the top 5 cm of the soil. Properties were least favourable for infiltration at the grazed site, with the greatest bulk density, least macroporosity and hydraulic conductivity or greatest pore tortuosity. In general, spatial variation in zones with restricted and good hydraulic conductivity together with reduced aggregate sorptivity in the deeper horizons made the soil prone to preferential flow when initially dry. Prolonged wetness, on the other hand, reduced saturated hydraulic conductivity significantly, resulting in surface run‐off. Harvesting was considered the best management practice due to its inherent capacity for reducing the soil nutrient content and because it has minor implications for soil physical properties.
MicroFilament Analyzer, an image analysis tool for quantifying fibrillar orientation, reveals changes in microtubule organization during gravitropism
Authors: Jacques Eveline , Buytaert Jan , Wells Darren M. , Lewandowski Michal , Bennett Malcolm J. , Dirckx Joris , Verbelen Jean‐Pierre , Vissenberg Kris
Published: March 2013

Image acquisition is an important step in the study of cytoskeleton organization. As visual interpretations and manual measurements of digital images are prone to errors and require a great amount of time, a freely available software package named MicroFilament Analyzer (MFA) was developed. The goal was to provide a tool that facilitates high‐throughput analysis to determine the orientation of filamentous structures on digital images in a more standardized, objective and repeatable way. Here, the rationale and applicability of the program is demonstrated by analyzing the microtubule patterns in epidermal cells of control and gravi‐stimulated Arabidopsis thaliana roots. Differential expansion of cells on either side of the root results in downward bending of the root tip. As cell expansion depends on the properties of the cell wall, this may imply a differential orientation of cellulose microfibrils. As cellulose deposition is orchestrated by cortical microtubules, the microtubule patterns were analyzed. The MFA program detects the filamentous structures on the image and identifies the main orientation(s) within individual cells. This revealed four distinguishable microtubule patterns in root epidermal cells. The analysis indicated that gravitropic stimulation and developmental age are both significant factors that determine microtubule orientation. Moreover, the data show that an altered microtubule pattern does not precede differential expansion. Other possible applications are also illustrated, including field emission scanning electron micrographs of cellulose microfibrils in plant cell walls and images of fluorescent actin.
Closed cycle chiller as a low cost alternative to liquid nitrogen in molecular beam epitaxy
Authors: Lewis Ryan B. , Mackenzie James A. , Tiedje Thomas , Beaton Daniel A. , Masnadi-Shirazi Mostafa , Bahrami-Yekta Vahid , Watkins Keelan P. , Mooney Patricia M.
Published: March 2013

The high cost of cooling the cryoshroud in a molecular beam epitaxy system has been greatly reduced by replacing liquid nitrogen (LN2) as a coolant with a silicone polymer heat transfer fluid cooled to as low as −80 °C by a closed cycle chiller. Gallium arsenide epitaxial layers have been grown with two different cooling configurations of the shroud: conventional LN2 cooling and cooling to −70 °C with the chiller. The partial pressure of water in the chamber is a factor of about 2.5 higher with the closed cycle chiller operating at −70 °C than with liquid nitrogen in the shroud. No significant difference is observed in the density of deep levels in the GaAs, as determined by deep level transient spectroscopy.
Estimating the viscoelastic modulus of a thrombus using an ultrasonic shear‐wave approach
Authors: Huang Chih‐Chung , Chen Pay‐Yu , Shih Cho‐Chiang
Published: March 2013

Purpose:

Measurements of the viscoelastic properties of a thrombus can be used to assess whether blood clots are likely to become occlusive or to break apart and leak into the blood circulation and block smaller vessels. An accurate method for estimating both the shear elasticity and viscosity of a blood clotin vivo is still lacking, which prompted us to use a novel shear‐wave approach to measure the viscoelastic modulus of blood clots.

Methods:

The shear‐wave dispersion ultrasound vibrometry was used to measure both the elasticity and viscosity of blood clots. The experimental system was verified by measuring the viscoelastic modulus of phantoms containing gelatin at different concentrations. Blood‐clot experiments were carried out using porcine whole blood with hematocrits ranging from 3% to 40%. The measured values for both clots and gelatin phantoms were compared to those obtained using an embedded‐sphere method in order to validate the accuracy of the viscoelastic modulus estimations.

Results:

The shear elastic modulus increased from 406.9 ± 15.8 (mean ± SD) Pa for 3% gelatin to 1587.2 ± 28.9 Pa for 7% gelatin, while the viscosity increased from 0.12 ± 0.02 Pa s to 0.86 ± 0.05 Pa s, respectively. The shear modulus increased from 196.8 ± 58.4 Pa for 40%‐hematocrit clots to 641.4 ± 76.3 Pa for 3%‐hematocrit clots, while the viscosity increased from 0.29 ± 0.02 Pa s to 0.42 ± 0.01 Pa s, respectively.

Conclusions:

The results from the statistical analysis indicated that both the embedded‐sphere and shear‐wave approaches can provide accurate estimations of the shear elasticity for clots and gelatin phantoms. In contrast, the shear‐wave approach as well as other methods of rheological measurements does not provide accurate viscosity estimations for blood clots. However, the measured viscosity range of 0.29–0.42 Pa s is reasonable for blood clots.
First study of on‐treatment volumetric imaging during respiratory gated VMAT
Authors: Choi Kihwan , Xing Lei , Koong Albert , Li Ruijiang
Published: March 2013

Purpose:

To obtain on‐treatment volumetric patient anatomy during respiratory gated volumetric modulated arc therapy (VMAT).

Methods:

On‐board imaging device integrated with Linacs offers a viable tool for obtaining patient anatomy during radiation treatment delivery. In this study, the authors acquired beam‐level kV images during gated VMAT treatments using a Varian TrueBeam™STx Linac. These kV projection images are triggered by a respiratory gating signal and can be acquired immediately before treatment MV beam on at every breathing cycle during delivery. Because the kV images are acquired with an on‐board imaging device during a rotational arc therapy, they provide the patient anatomical information from many different angles or projection views (typically 20–40). To reconstruct the volumetric image representing patient anatomy during the VMAT treatment, the authors used a compressed sensing method with a fast first‐order optimization algorithm. The conventional FDK reconstruction was also used for comparison purposes. The method was tested on a dynamic anthropomorphic physical phantom as well as a lung patient.

Results:

The reconstructed volumetric images for a dynamic anthropomorphic physical phantom and a lung patient showed clearly visible soft‐tissue target as well as other anatomical structures, with the proposed compressed sensing‐based image reconstruction method. Compared with FDK, the compressed sensing method leads to a ∼two and threefold increase in contrast‐to‐noise ratio around the target area in the phantom and patient case, respectively.

Conclusions:

The proposed technique provides on‐treatment volumetric patient anatomy, with only a fraction (<10%) of the imaging dose used in conventional CBCT procedures. This anatomical information may be valuable for geometric verification and treatment guidance, and useful for verification of treatment dose delivery, accumulation, and adaptation in the future.
Depth-based signal separation with vertical line arrays in the deep ocean
Authors: McCargar Reid , Zurk Lisa M.
Published: March 2013

Deep vertical line arrays can exploit the reliable acoustic path (RAP), which provides low transmission loss (TL) for targets at moderate ranges, and increased TL for distant interferers. However, nearby surface interference also has favorable RAP propagation and cannot be separated from a submerged target without horizontal aperture. In this work, a physics-based Fourier transform variant is introduced, which achieves depth-based signal separation by exploiting the spatial structure resulting from the coherent addition of the direct and surface-reflected propagation paths present for submerged sources. Simulation results demonstrate depth-based signal separation without requiring knowledge of the ocean environment.
Light for All Reasons: Versatility in the Behavioral Repertoire of the Flashlight Fish
Authors: Morin James G. , Harrington Anne , Nealson Kenneth , Krieger Neil , Baldwin Thomas O. , Hastings J. W.
Published: March 2013

The flashlight fish,
Photoblepharon
, possesses headlight-like luminous organs situated in the orbit just below the eyes. On the basis of direct field and laboratory studies, it is postulated that the bioluminescence is used by the fish for many different functions: to assist in obtaining prey, to deter or escape predators, and for intraspecific communication. The fish also uses its light to see by.
The Surface Temperature of the Sun and Changes in the Solar Constant
Authors: Kuhn J. R. , Libbrecht K. G. , Dicke R. H.
Published: March 2013

The solar distortion telescope has been used to measure the limb shape and latitude dependence of the limb brightness during the summer months for a 5-year period—a time base sufficient to detect solar cycle trends in the data. Comparison of these observations with spaceborne measurements of the solar constant suggests that a significant part of the solar cycle variation in irradiance is a result of temporal changes in the latitude-dependent surface temperature of the sun.
Enhancement of Surface Cooling Due to Forest Fire Smoke
Authors: Robock Alan
Published: March 2013

Smoke emitted from forest fires in northern California in September 1987 was trapped in a valley by an inversion for 3 weeks. Daily maximum temperatures on the valley floor were more than 15°C below normal for 1 week and more than 5°C below normal for 3 weeks. The smoke strengthened the inversion by preventing surface warming by solar radiation, thereby enhancing the smoke trapping and the surface cooling in a positive feedback loop. These results may have implications for nuclear winter.
Early Insect Diversification: Evidence from a Lower Devonian Bristletail from Québec
Authors: Labandeira Conrad C. , Beall Bret S. , Hueber Francis M.
Published: March 2013

The earliest insect for which there is significant structural data, a bristletail (Archaeognatha) from the Early Devonian (Emsian Stage) of the Gaspé Peninsula of Québec, Canada, is described. Detailed analysis of the head indicates that this insect had large, bulging, separated, compound eyes, monocondylic mandibles, and numerous sensory setae. This fossil, the oldest record of terrestrial animal life from North America, suggests that early hexapod diversification occurred contemporaneously with the emergence of the first vascular land plants during the Silurian.
VirD2 Protein of
Agrobacterium tumefaciens
Very Tightly Linked to the 5' End of T-Strand DNA
Authors: Ward Eric R. , Barnes Wayne M.
Published: March 2013

The T-strand, a probable intermediate of
Agrobacterium
plant transformation, is bound by a nondenaturable linkage to a protein moiety at its 5′ end. The protein is shown to be the polypeptide VirD2, previously identified as a component of the T-DNA border endonuclease that initiates T-strand production. T-strands from an
Agrobacterium strain
expressing a
virD2-lacZ
fusion are bound to a protein of larger size than the wild-type protein and are immunoprecipitable by antibody to β-galactosidase.
Atmospheric Evolution of the Terrestrial Planets
Authors: Hunten Donald M.
Published: March 2013

The major atmospheric gases on Earth, Venus, and Mars were probably CO
2
, H
2
O, and N
2
. Most of the Earth's CO
2
is tied up in minerals such as limestone, and Venus has lost most of its H
2
O, leaving the CO
2
in the atmosphere. Much of Mars' atmosphere may have been eroded in impacts by large meteoroids early in solar-system history. Noble gases are very underabundant everywhere, and must have been lost during an early period; they were probably dragged along during rapid loss of massive amounts of hydrogen. The tenuous atmospheres of Mercury and the moon have lifetimes of a few days or less and must be continuously replenished from internal or external sources.
The Ice Record of Greenhouse Gases
Authors: Raynaud D. , Jouzel J. , Barnola J. M. , Chappellaz J. , Delmas R. J. , Lorius C.
Published: March 2013

Gases trapped in polar ice provide our most direct record of the changes in greenhouse gas levels during the past 150,000 years. The best documented trace-gas records are for CO
2
and CH
4
. The measurements corresponding to the industrial period document the recent changes in growth rate. The variability observed over the last 1000 years constrains the possible feedbacks of a climate change on the trace gases under similar conditions as exist today. Changes in the levels of greenhouse gases during the glacial-interglacial cycle overall paralleled, at least at high southern latitudes, changes in temperature; this relation suggests that greenhouse gases play an important role as an amplifier of the initial orbital forcing of Earth's climate and also helps to assess the feedbacks on the biogeochemical cycles in a climate system in which the components are changing at different rates.
The Global Carbon Dioxide Budget
Authors: Sundquist Eric T.
Published: March 2013

The increase in atmospheric CO
2
levels during the last deglaciation was comparable in magnitude to the recent historical increase. However, global CO
2
budgets for these changes reflect fundamental differences in rates and in sources and sinks. The modern oceans are a rapid net CO
2
sink, whereas the oceans were a gradual source during the deglaciation. Unidentified terrestrial CO
2
sinks are important uncertainties in both the deglacial and recent CO
2
budgets. The deglacial CO
2
budget represents a complexity of long-term dynamic behavior that is not adequately addressed by current models used to forecast future atmospheric CO
2
levels.
Identification of the Receptor-Binding Protein in Lytic Leuconostoc pseudomesenteroides Bacteriophages
Authors: Kot Witold , Hammer Karin , Neve Horst , Vogensen Finn K.
Published: March 2013

Two phages, P793 and ΦLN04, sharing 80.1% nucleotide sequence identity but having different strains of
Leuconostoc pseudomesenteroides
as hosts, were selected for identification of the host determinant gene. Construction of chimeric phages leading to the expected switch in host range identified the host determinant genes as ORF21
P793
/ORF23
ΦLN04
. The genes are located in the tail structural module and have low sequence similarity at the distal end.
Loss of Culturability of Salmonella enterica subsp. enterica Serovar Typhimurium upon Cell-Cell Contact with Human Fecal Bacteria
Authors: Avendaño-Pérez Gaspar , Pin Carmen
Published: March 2013

Loss of culturability of
Salmonella enterica
subsp.
enterica
serovar Typhimurium has been observed in mixed cultures with anaerobic fecal bacteria under conditions that allow local interaction between cells, such as cell contact. A reduction of a population of culturable
S.
Typhimurium on the order of ∼10
4
to 10
5
CFU/ml was observed in batch anaerobic mixed cultures with fecal samples from different human donors. Culturability was not affected either in supernatants collected at several times from fecal cultures, when separated from fecal bacteria by a membrane of 0.45-μm pore size, or when in contact with inactivated fecal bacterial cells. Loss of culturability kinetics was characterized by a sharp reduction of several logarithmic units followed by a pronounced tail. A mathematical model was developed to describe the rate of loss of culturability as a function of the frequency of encounters between populations and the probability of inactivation after encounter. The model term
F
(
S
·
F
)
1/2
quantifies the effect of the concentration of both populations, fecal bacteria (
F
) and
S.
Typhimurium (
S
), on the loss of culturability of
S.
Typhimurium by cell contact with fecal bacteria. When the value of
F
(
S
·
F
)
1/2
decreased below ca. 10
15
(CFU/ml)
2
, the frequency of encounters sharply decreased, leading to the deceleration of the inactivation rate and to the tailing off of the
S.
Typhimurium population. The probability of inactivation after encounter,
P
, was constant, with an estimated value of ∼10
−5
for all data sets.
P
might be characteristic of the mechanism of growth inhibition after a cell encounter.
3′ Truncation of the
GPD1
Promoter in Saccharomyces cerevisiae for Improved Ethanol Yield and Productivity
Authors: Ding Wen-Tao , Zhang Guo-Chang , Liu Jing-Jing
Published: March 2013

Glycerol is a major by-product in bioethanol fermentation by the yeast
Saccharomyces cerevisiae
, and decreasing glycerol formation for increased ethanol yield has been a major research effort in the bioethanol field. A new strategy has been used in the present study for reduced glycerol formation and improved ethanol fermentation performance by finely modulating the expression of
GPD1
in the KAM15 strain (
fps1
Δ
pPGK1-GLT1 gpd2
Δ). The
GPD1
promoter was serially truncated from the 3′ end by 20 bp to result in a different expression strength of
GPD1
. The two engineered promoters carrying 60- and 80-bp truncations exhibited reduced promoter strength but unaffected osmostress response. These two promoters were integrated into the KAM15 strain, generating strains LE34U and LE35U, respectively. The transcription levels of LE34U and LE35U were 37.77 to 45.12% and 21.34 to 24.15% of that of KAM15U, respectively, depending on osmotic stress imposed by various glucose concentrations. In very high gravity (VHG) fermentation, the levels of glycerol for LE34U and LE35U were reduced by 15.81% and 30.66%, respectively, compared to KAM15U. The yield and final concentration of ethanol for LE35U were 3.46% and 0.33% higher, respectively, than those of KAM15U. However, fermentation rate and ethanol productivity for LE35U were reduced. On the other hand, the ethanol yield and final concentration for LE34U were enhanced by 2.28% and 2.32%, respectively, compared to those of KAM15U. In addition, a 2.31% increase in ethanol productivity was observed for LE34U compared to KAM15U. These results verified the feasibility of our strategy for yeast strain development.
“Candidatus Midichloriaceae” fam. nov. (Rickettsiales), an Ecologically Widespread Clade of Intracellular Alphaproteobacteria
Authors: Montagna Matteo , Sassera Davide , Epis Sara , Bazzocchi Chiara , Vannini Claudia , Lo Nathan , Sacchi Luciano , Fukatsu Takema , Petroni Giulio , Bandi Claudio
Published: March 2013

“
Candidatus
Midichloria mitochondrii” is an intramitochondrial bacterium of the order
Rickettsiales
associated with the sheep tick
Ixodes ricinus
. Bacteria phylogenetically related to “
Ca
. Midichloria mitochondrii” (midichloria and like organisms [MALOs]) have been shown to be associated with a wide range of hosts, from amoebae to a variety of animals, including humans. Despite numerous studies focused on specific members of the MALO group, no comprehensive phylogenetic and statistical analyses have so far been performed on the group as a whole. Here, we present a multidisciplinary investigation based on 16S rRNA gene sequences using both phylogenetic and statistical methods, thereby analyzing MALOs in the overall framework of the
Rickettsiales
. This study revealed that (i) MALOs form a monophyletic group; (ii) the MALO group is structured into distinct subgroups, verifying current genera as significant evolutionary units and identifying several subclades that could represent novel genera; (iii) the MALO group ranks at the level of described
Rickettsiales
families, leading to the proposal of the novel family “
Candidatus
Midichloriaceae.” In addition, based on the phylogenetic trees generated, we present an evolutionary scenario to interpret the distribution and life history transitions of these microorganisms associated with highly divergent eukaryotic hosts: we suggest that aquatic/environmental protista have acted as evolutionary reservoirs for members of this novel family, from which one or more lineages with the capacity of infecting metazoa have evolved.
Schizosaccharomyces pombe Disaggregation Machinery Chaperones Support Saccharomyces cerevisiae Growth and Prion Propagation
Authors: Reidy Michael , Sharma Ruchika , Masison Daniel C.
Published: March 2013

Hsp100 chaperones protect microorganisms and plants from environmental stress by cooperating with Hsp70 and its nucleotide exchange factor (NEF) and Hsp40 cochaperones to resolubilize proteins from aggregates. The
Saccharomyces cerevisiae
Hsp104 (Sc-Hsp104)-based disaggregation machinery also is essential for replication of amyloid-based prions.
Escherichia coli
ClpB can substitute for Hsp104 to propagate [
PSI
+
] prions in yeast, but only if
E. coli
DnaK and GrpE (Hsp70 and NEF) are coexpressed. Here, we tested if the reported inability of
Schizosaccharomyces pombe
Hsp104 (Sp-Hsp104) to support [
PSI
+
] propagation was due to similar species-specific chaperone requirements and find that Sp-Hsp104 alone supported propagation of three different yeast prions. Sp-Hsp70 and Sp-Fes1p (NEF) likewise functioned in place of their
Sa. cerevisiae
counterparts. Thus, chaperones of these long-diverged species possess conserved activities that function in processes essential for both cell growth and prion propagation, suggesting
Sc. pombe
can propagate its own prions. We show that curing by Hsp104 overexpression and inactivation can be distinguished and confirm the observation that, unlike Sc-Hsp104, Sp-Hsp104 cannot cure yeast of [
PSI
+
] when it is overexpressed. These results are consistent with a view that mechanisms underlying prion replication and elimination are distinct.
Complete Genome Sequence of
Escherichia
Phage ADB-2 Isolated from a Fecal Sample of Poultry
Authors: Bhensdadia D. V. , Bhimani H. D. , Rawal C. M. , Kothari V. V. , Raval V. H. , Kothari C. R. , Patel A. B. , Bhatt V. D. , Parmar N. R. , Sajnani M. R. , Koringa P. G. , Joshi C. G. , Singh S. P. , Kothari R. K.
Published: March 2013

Escherichia
phage ADB-2 was isolated from a chicken fecal sample. It is a virulent phage and shows effective inhibition of
Escherichia coli
strains. Here we announce the completely sequenced genome of
Escherichia
phage ADB-2, and major findings from its annotation are described.
Complete Genome Sequence of Mycobacterium bovis BCG Korea, the Korean Vaccine Strain for Substantial Production
Authors: Joung Sun Myung , Jeon Sung Joo , Lim Young Ju , Lim Jong-Sung , Choi Beom-Soon , Choi Ik-Young , Yu Jeong Hee , Na Kyung-In , Cho En-Hi , Shin Sang-Sook , Park Young Kil , Kim Chang-Ki , Kim Hee-Jin , Ryoo Sung Weon
Published: March 2013

Mycobacterium bovis
bacillus Calmette-Guérin (BCG) is the only vaccine available against tuberculosis, and the strains used worldwide represent a family of daughter strains with distinct genotypic characteristics. Here, we report the complete genome sequence of
M. bovis
BCG Korea, the strain that will be actually used in Korea for vaccine production.
Whole-Genome Sequences of an Aerobic Anoxygenic Phototroph,
Blastomonas
sp. Strain AAP53, Isolated from a Freshwater Desert Lake in Inner Mongolia, China
Authors: Zeng Yonghui , Koblížek Michal , Feng Fuying , Liu Yapeng , Wu Zaohe , Jian Jichang
Published: March 2013

Blastomonas
is a strictly aerobic bacteriochlorophyll
a
-producing genus within the alpha-4
Proteobacteria
. Here we report the first genome sequence from this genus. The draft genome of
Blastomonas
sp. strain AAP53 contains a split photosynthesis gene cluster and two gene clusters encoding a flagellar system. Genes for the autotrophic CO
2
fixation pathway are absent.
Draft Genome of the Marine Gammaproteobacterium Halomonas titanicae
Authors: Sánchez-Porro Cristina , de la Haba Rafael R. , Cruz-Hernández Norge , González Juan M. , Reyes-Guirao Cristina , Navarro-Sampedro Laura , Carballo Modesto , Ventosa Antonio
Published: March 2013

Halomonas titanicae
strain BH1 is a heterotrophic, aerobic marine bacterium which was isolated from rusticles of the RMS Titanic wreck. Here we report the draft genome sequence of this halophilic gammaproteobacterium.
DsbA and MgrB Regulate
steA
Expression through the Two-Component System PhoQ/PhoP in Salmonella enterica
Authors: Cardenal-Muñoz Elena , Ramos-Morales Francisco
Published: March 2013

SteA is a protein that can be translocated into host cells through the two virulence-related type III secretion systems that are present in
Salmonella enterica
. We used the T-POP system to carry out general screens for loci that exhibited activation or repression of a
steA
::
lacZ
fusion. These screens identified the histidine kinase PhoQ and the response regulator PhoP as positive regulators of
steA
. Transcription of this gene is σ70 dependent, and the promoter of
steA
contains a PhoP-binding site that mediates direct regulation by PhoP. Our screens also detected MgrB (also known as YobG) as a negative regulator of the expression of
steA
. Disruption of the gene encoding the periplasmic disulfide oxidoreductase DsbA or addition of the reducing agent dithiothreitol increases transcription of
steA
. The effects of MgrB and DsbA on
steA
are mediated by PhoP. These results suggest that the cellular redox status is a factor contributing to regulation of
steA
and, probably, other virulence genes regulated by the PhoQ/PhoP two-component system.
Genomic Reconstruction of the Transcriptional Regulatory Network in Bacillus subtilis
Authors: Leyn Semen A. , Kazanov Marat D. , Sernova Natalia V. , Ermakova Ekaterina O. , Novichkov Pavel S. , Rodionov Dmitry A.
Published: March 2013

The adaptation of microorganisms to their environment is controlled by complex transcriptional regulatory networks (TRNs), which are still only partially understood even for model species. Genome scale annotation of regulatory features of genes and TRN reconstruction are challenging tasks of microbial genomics. We used the knowledge-driven comparative-genomics approach implemented in the RegPredict Web server to infer TRN in the model Gram-positive bacterium
Bacillus subtilis
and 10 related
Bacillales
species. For transcription factor (TF) regulons, we combined the available information from the DBTBS database and the literature with bioinformatics tools, allowing inference of TF binding sites (TFBSs), comparative analysis of the genomic context of predicted TFBSs, functional assignment of target genes, and effector prediction. For RNA regulons, we used known RNA regulatory motifs collected in the Rfam database to scan genomes and analyze the genomic context of new RNA sites. The inferred TRN in
B. subtilis
comprises regulons for 129 TFs and 24 regulatory RNA families. First, we analyzed 66 TF regulons with previously known TFBSs in
B. subtilis
and projected them to other
Bacillales
genomes, resulting in refinement of TFBS motifs and identification of novel regulon members. Second, we inferred motifs and described regulons for 28 experimentally studied TFs with previously unknown TFBSs. Third, we discovered novel motifs and reconstructed regulons for 36 previously uncharacterized TFs. The inferred collection of regulons is available in the RegPrecise database (
http://regprecise.lbl.gov/
) and can be used in genetic experiments, metabolic modeling, and evolutionary analysis.
Archaeal DNA Polymerase D but Not DNA Polymerase B Is Required for Genome Replication in Thermococcus kodakarensis
Authors: Čuboňová Lubomira , Richardson Tomas , Burkhart Brett W. , Kelman Zvi , Connolly Bernard A. , Reeve John N. , Santangelo Thomas J.
Published: March 2013

Three evolutionarily distinct families of replicative DNA polymerases, designated polymerase B (Pol B), Pol C, and Pol D, have been identified. Members of the Pol B family are present in all three domains of life, whereas Pol C exists only in
Bacteria
and Pol D exists only in
Archaea
. Pol B enzymes replicate eukaryotic chromosomal DNA, and as members of the Pol B family are present in all
Archaea
, it has been assumed that Pol B enzymes also replicate archaeal genomes. Here we report the construction of
Thermococcus kodakarensis
strains with mutations that delete or inactivate key functions of Pol B.
T. kodakarensis
strains lacking Pol B had no detectable loss in viability and no growth defects or changes in spontaneous mutation frequency but had increased sensitivity to UV irradiation. In contrast, we were unable to introduce mutations that inactivated either of the genes encoding the two subunits of Pol D. The results reported establish that Pol D is sufficient for viability and genome replication in
T. kodakarensis
and argue that Pol D rather than Pol B is likely the replicative DNA polymerase in this archaeon. The majority of
Archaea
contain Pol D, and, as discussed, if Pol D is the predominant replicative polymerase in
Archaea
, this profoundly impacts hypotheses for the origin(s), evolution, and distribution of the different DNA replication enzymes and systems now employed in the three domains of life.
Controlling Practitioner–patient Relationships in Acupuncture Trials: A Systematic Review and Meta-Regression
Authors: Prady Stephanie L , Burch Jane , Crouch Simon , MacPherson Hugh
Published: March 2013

Background

In trials, ‘therapist intensive’ complex interventions are typically delivered over time, during which a relationship between the practitioner and participant may develop. Such relationships are sometimes criticised as obscuring any ‘true’ treatment effect. Limiting interactions is one strategy that might be used to try to control for the effect of a therapeutic relationship.

Objectives

We conducted systematic review into the rationale, methods and effects of constraining relationships in controlled trials and cohort studies of acupuncture, including studies published before 2008 with an update citation search in 2010.

Methods

We searched six databases without keyword restrictions. Meta-analysis and meta-regression were used to explore the effect of relationship constraint on pain outcomes.

Results

Eighty-one of 785 (10.3%) trials reported constraining relationships. Most did not state the reason for constraint, describe the nature of the limitation, provide information on how the constrained relationship was monitored or note protocol adherence. Where a reason was reported, this was primarily to maintain participant blinding, rarely was it stated that the constraint was to control the therapeutic relationship. We found no evidence of an effect of constraint on pain outcomes (percentage heterogeneity explained, p=0.89). These results were robust to variation in trial quality and design.

Conclusions

Acupuncture trials appear to be constrained mostly to try to prevent participant unblinding to their allocated treatment, not to control the therapeutic relationship. The apparent lack of monitoring and negligible effects on pain outcomes of the included trials indicate the need for more high-quality randomised controlled trials investigating the effect of constraint.
The known unknowns of perioperative stroke during carotid body tumour resection
Authors: Joshi Meera , Lattimer Christopher R , Shah Bareen , Geroulakos George
Published: March 2013

Carotid body tumour (CBT) surgery has a risk of stroke. A 57-year-old lady presented with lethargy and generalised limb pain secondary to a right parathyroid adenoma. CT scan demonstrated as an incidental finding of a left CBT. Intraoperatively the CBT was infiltrating the vessel wall. The carotid bifurcation was resected and reconstructed using a reversed saphenous vein graft. Postoperatively the patient developed right arm weakness. A CT scan showed a left hemispheric watershed infarct. On discharge (day 8 postoperatively) she had no functional deficit. Reconstruction of the internal carotid artery in patients with CBT is associated with an increased risk of stroke. This index case and literature research highlight the knowns and unknowns on stroke associated with CBT resection.
Cauda equina syndrome: the importance of complete multidisciplinary team management
Authors: Shivji Faiz , Tsegaye Magnum
Published: March 2013

A 44-year-old lady with a history of lumbar back pain presented to the emergency department complaining of severe back pain radiating to her buttocks. Positive examination findings were a loss of sensation in the perianal area and 348 ml of retained urine. An urgent MRI showed compression of the cauda equina by a herniated disc. The patient was operated upon that evening, having a lumbar 5/sacral 1 decompression and sequestrectomy. During follow-up, the patient was reviewed by a consultant spinal surgeon, a urologist and our cauda equina nurse at every appointment, as per the cauda equina pathway specifically designed and implemented by our spinal unit. This report shows the complex nature of cauda equina syndrome and broad functional deficit patients can suffer from. It shows the benefits of prompt diagnosis and surgery, together with intensive, multidisciplinary follow-up and treatment, all of which are possible by a specially created, cauda equina protocol.
A conversion disorder or a stroke? A proximal basilar artery thrombosis induced ‘locked-in’ syndrome in a young Caucasian woman
Authors: Li Wang , Brandon Ohman , Smith Debbie Villarreal , Petersen Eric
Published: March 2013

The incidence of the basilar artery occlusion is relatively low among all strokes. Clinical presentation varies depending on the location of the occlusion. The symptoms include mild dysarthria to coma or sudden death. The initial subtle clinical presentation could lead to misdiagnosis. Psychogenic diagnosis in the differential could make the timely diagnosis more difficult. This case involves a 34-year-old woman presenting with a gradual onset of slurred speech. The initial CT scan of head did not indicate any intracranial pathology, and she was initially treated for an anxiety/conversion disorder. With progression of the pathology, the patient quickly developed a ‘locked-in’ syndrome, with preserved high cognitive function and vertical eye movement, but otherwise total loss of motor function. The diagnosis was confirmed with MRI/MR angiography studies, which indicated thrombosis of the proximal basilar artery. Serological studies did not disclose any relevant risk factors.
Missing red flags in back pain—tuberculosis of the spine: an important differential for back pain in non-endemic countries
Authors: Edwards Matt Alwyn , Hawkins Melanie , Alao David
Published: March 2013

Chronic back pain is an extremely common complaint. All primary care physicians will be on the lookout for the ‘red flags’ that suggest serious pathology. The diagnosis of spinal infection with tuberculosis (TB) is uncommon and often not considered, especially in areas where the rate is very low such as the south west of England. We describe a patient presenting to the emergency department with severe pain, immobility and with a sensory deficit level. Unfortunately, given the favourable results for early medical treatment for spinal TB, this patient presented late and had a very poor outcome.
Recurrent facial hemiparesis due to dolichoectatic vertebrobasilar artery: an unusual and ignored cause
Authors: Mishra Vijay Nath , Chaurasia Rameshwar Nath , Gupta Shailesh , Joshi Deepika
Published: March 2013

Dolichoectatic arteries are elongated tortuous aneurysms of intracranial arteries most commonly of vertebrobasilar tree presenting with ischaemic, haemorrhagic, thromboembolic lesions or with cranial nerve compression. The clinical presentation includes tic douloureux, neuralgia, tinnitus, vertigo, motor or sensory deficits, ataxia, dementia, Parkinsonism, hydrocephalus, headache, migraine, aneurysm, neoplasm, stroke/transient ischaemic attacks, leukoencephalopathy, central sleep apnoea and cerebellar dysfunctions. We present a case of recurrent facial nerve palsy secondary to vertebrobasilar dolichoectasia, an interesting and rare condition.
Temporary arterial stenting in a full-house spaghetti wrist injury in a remote rural setting: benefit for hand perfusion or risk of increased morbidity?
Authors: Bauer Stefan , Savundra James
Published: March 2013

We report a case of temporary arterial plastic tube stenting of the ulnar and radial artery in a complete spaghetti wrist injury in a remote rural setting. Exploration in a specialist centre 18 h postinjury revealed that the tubes were clotted off with adjacent thrombi but hand perfusion was maintained. Intimal damage required vein grafting of both arteries 24 h postinjury. Hand perfusion was not compromised at follow-up. This case highlights that arterial hand perfusion can be maintained without the ulnar and radial artery. Arterial manipulation and tube insertion outside a specialist centre bears the risk of increased morbidity and potential microembolism and must therefore not be attempted.
A rare occurrence of peripheral ossifying fibroma in the first decade of life and its management
Authors: Vyawahare Saket , Banda Naveen Reddy , Barodiya Animesh , Banda Vanaja Reddy
Published: March 2013

Retracted due to duplicate publication.
A cohort study for the impact of activity-limiting injuries based on the Canadian National Population Health Survey 1994–2006
Authors: Mo Frank , Neutel Ineke C , Morrison Howard , Hopkins Doug , Da Silva Caroline , Jiang Ying
Published: March 2013

Objective

To examine the prevalence and factors affecting activity-limiting injuries (ALI) in individuals and in the Canadian population; to estimate the short and long term impact on health status and well-being because of ALI in Canada from 1994 to 2006 using the Canadian National Population Health Survey (NPHS).

Design

The NPHS is a randomised longitudinal cohort study with biennial interviews, with information on age, sex, education, marital status, income, residence, height and weight to self-perceived health status, healthcare utilisation and medication use in addition to ALI.

Setting

The study population was a random sample of male and female participants 20 years and older from 10 provinces and three territories in Canada.

Primary and secondary outcome measures

Logistic regression models were used to assess the potential impact of ALI on individuals and on the Canadian population. The interviews 2 years before and 2 years after the ALI were compared to examine long-term effects, and the McNemar test option in SAS was used for the matched analysis.

Results

The immediate impacts of ALI were pain, disability and disruption of regular life. Long-term effects in patients were chronic pain and increased medical doctor visits. Population impact included a considerable increase in healthcare access and cost. The odds ratios (OR) for the 20–39 age group compared with those 60+ was 2.2; 95% CI 1.8 to 2.7, while the OR associated with male participants was 1.4; 95% CI 1.1 to 1.6. Individuals consuming nine or more alcoholic drinks per week were also significantly more likely to report an ALI (OR, 1.5; 95% CI 1.3 to 1.8).

Conclusions

The findings from this study illustrated the immediate and long-term impact of individuals and population level injuries in Canada. Injury control policies should aim to prevent the number of injuries, fatalities as well as the consequences among survivors.