bluuebunny/crossref_metadata_2025 huggingface dataset:
Improved In Vivo Performance of Second‐Generation Cryoballoon for Pulmonary Vein Isolation
Authors: COULOMBE NICOLAS , PAULIN JAIME , SU WILBER
Published: April 2013

Coulombe—Improved Performance of Second‐Generation Cryoballoon

Introduction

A novel cryoballoon with improved refrigerant distribution promises better pulmonary vein (PV) isolation success rate without sacrificing the technology's safety profile. This study aimed to compare the Arctic Front® (AF) balloon to the new Arctic Front Advance™ (AFA).

Methods and Results

Twenty pulmonary PVs from 10 healthy dogs weighing 29.8 ± 1.1 kg were assigned to ablation with AF and AFA, using a 23 mm or 28 mm balloon. A single 4‐minute ablation was performed in each vessel, with no phrenic nerve monitoring. The Achieve™ mapping catheter was used to confirm acute isolation. Thirty days post‐treatment the ablation sites were assessed for electrical PV isolation and ablation completeness via gross and histological examination. The phrenic nerve, PVs, lungs, esophagus, kidneys, and brain were collected for evaluation of potential damage. A preprocedural and prenecropsy CT were performed to assess incidence of PV stenosis. All 10 PVs were fully isolated with AFA; 6 of 10 PVs were fully isolated with AF. In all cases, lesion gaps with AF are believed to stem from inadequate cooling of the most distal balloon segment that was in contact with the unablated PV tissue. No untoward findings were detected on gross examination of the heart, esophagus, kidneys, brain, or PVs. One phrenic nerve had cross‐sectional ablation associated with an AFA 23 mm balloon. Superficial regions of subpleural lung fibrosis were noted adjacent to 7 PVs.

Conclusions

PV isolation and lesion completeness were improved with Arctic Front Advance, while no unexpected findings were found related to safety.
Management of advanced non‐melanoma skin cancers using helical tomotherapy
Authors: Kramkimel N. , Dendale R. , Bolle S. , Zefkili S. , Fourquet A. , Kirova Y.M.
Published: April 2013

Background

Helical tomotherapy (HT) is a relatively new method of radiotherapy, the main advantages of which are an increase of irradiation dose on the target tumour volume and best protection of adjacent organs at risk.

Objective

To provide an accurate evaluation of efficiency and tolerance of HT on different kinds of non‐melanoma skin tumours.

Patients and methods

We analysed, retrospectively, 25 patients (pts) who were treated with HT for advanced non‐melanoma skin cancers. We studied the characteristics of patients and tumours, associated treatments, characteristics, efficacy and tolerance of HT treatment.

Results

Eight had basal cell carcinoma, Eight had cutaneous squamous cell carcinoma, five Merkel cell carcinoma and four adnexal carcinoma. The median age was 75 years (range 51–89). The median follow‐up was 12 months. HT was used because of incomplete excision (n = 12), lymph node involvement (n = 6), non‐operable lesions (n = 4) and high risk of relapse (n = 4). The delivered dose for the tumour bed was between 50 and 70 Gy and for the lymph node it was between 50 and 64 Gy. There was no grade III–IV adverse event, except one grade III mucositis. Fourteen pts suffered from limited toxic effects 6 months after the end of the treatment, mainly loss of eyebrow and teared eye. Complete remission was noticed for 22 pts (88%); one pt had progressive disease and two pts died.

Conclusion

HT is an effective option for advanced non‐melanoma skin cancers as radical treatment or in association with surgery. Early and late toxicity and cosmetic results are acceptable.
Source memory in normal aging and Parkinson's disease
Authors: Davidson Patrick S. R. , Cook Shaun P. , McGhan Leslie , Bouchard Thomas , Camicioli Richard
Published: April 2013

Several theorists have described memory in Parkinson's disease (PD) as involving an amplification of the deficits seen in normal aging, and drawn parallels between PD and frontal lesion patients. Both normal aging and frontal lobe damage impair memory for the context in which one has encountered information (i.e., source memory). We thus sought to determine whether PD patients would show especially poor source memory. We assessed memory for perceptual (voice), spatial (location of loudspeaker), and temporal (list) source memory in 18 PD patients, 23 healthy older adults, and 35 young people. Although both the healthy aged and PD groups performed more poorly than the young on most of the memory tests, the PD patients failed to show significantly greater impairments than the healthy older adults. The PD patients did perform more poorly, however, on a measure of executive function (the Wisconsin Card Sorting Test [WCST]). We discuss potential reasons why PD had a surprisingly minimal effect on source memory in our study, and relate our data to broader theories of memory impairment in Parkinson's disease.
Narcolepsy and pregnancy: a retrospective European evaluation of 249 pregnancies
Authors: Maurovich‐Horvat Eszter , Kemlink David , Högl Birgit , Frauscher Birgit , Ehrmann Laura , Geisler Peter , Ettenhuber Katharina , Mayer Geert , Peraita‐Adrados Rosa , Calvo Elena , Lammers Gert Jan , Van der Heide Astrid , Ferini‐Strambi Luigi , Plazzi Giuseppe , Poli Francesca , Dauvilliers Yves , Jennum Poul , Leonthin Helle , Mathis Johannes , Wierzbicka Aleksandra , Puertas Francisco J. , Beitinger Pierre A. , Arnulf Isabelle , Riha Renata L. , Tormášiová Maria , Slonková Jana , Nevšímalová Sona , Šonka Karel ,   the European Narcolepsy Network
Published: April 2013

In a retrospective cohort study undertaken in 12 European countries, 249 female narcoleptic patients with cataplexy (n = 216) and without cataplexy (n = 33) completed a self‐administrated questionnaire regarding pregnancy and childbirth. The cohort was divided further into patients whose symptoms of narcolepsy started before or during pregnancy (308 pregnancies) and those in whom the first symptoms of narcolepsy appeared after delivery (106 pregnancies). Patients with narcolepsy during pregnancy were older during their first pregnancy (P < 0.001) and had a higher body mass index (BMI) prior to pregnancy (P < 0.01). Weight gain during pregnancy was higher in narcoleptic patients with cataplexy (P < 0.01). More patients with narcolepsy–cataplexy during pregnancy had impaired glucose metabolism and anaemia. Three patients experienced cataplexy during delivery. The rate of caesarean sections was higher in the narcolepsy–cataplexy group compared to the narcolepsy group (P < 0.05). The mean birth weight and gestational age of neonates were within the normal range and did not differ across groups. Neonatal care was affected adversely by symptoms of narcolepsy in 60.1% of those with narcolepsy during pregnancy. This study reports more obstetric complications in patients with narcolepsy–cataplexy during pregnancy; however, these were not severe. This group also had a higher BMI and higher incidence of impaired glucose metabolism during pregnancy. Caesarian section was conducted more frequently in narcolepsy–cataplexy patients, despite cataplexy being a rare event during delivery. Furthermore, symptoms of narcolepsy may render care of the infant more difficult.
Poor sleep quality impairs cognitive performance in older adults
Authors: Miyata Seiko , Noda Akiko , Iwamoto Kunihiro , Kawano Naoko , Okuda Masato , Ozaki Norio
Published: April 2013

The prevalence of insomnia increases with age. Short sleep duration is associated with deficits in cognitive performance. We hypothesized that short sleep duration and sleep quality influence cognitive performance in older adults. The study included 78 adults aged 60 years and over (72.2 ± 5.9 years). Total sleep time and sleep efficiency (total sleep time/time in bed × 100) were calculated using actigraphy. We evaluated cognitive performance with the continuous performance test‐identical pairs and the number‐back test. Sleep apnea was evaluated overnight with a portable home monitoring system. The accuracy of the 0‐back test significantly decreased in participants with total sleep time less than 5 h compared with those with total sleep time greater than 7 h, but there was no significant difference in continuous performance test‐identical pairs between the two groups. Participants with sleep efficiency <85% showed a significant decrease in 0‐ and 1‐back test accuracy compared with those with sleep efficiency ≥85%. There were no significant differences in the accuracy of number‐back tests and continuous performance test‐identical pairs between apnea–hypopnea index ≥15 h−1 and apnea–hypopnea index <15 h−1 groups, or among lowest SpO2 ≥ 90%, lowest 80–90%, and lowest SpO2 < 80% groups. Age, total sleep time and sleep efficiency were significantly correlated with accuracy on the 0‐back test. Age and sleep efficiency were significantly correlated with accuracy on the 1‐back test. Multiple regression analysis revealed that total sleep time was independently correlated with accuracy on the 0‐back test, while age was independently correlated with accuracy on the 1‐back test. Our findings suggest that sleep duration and sleep quality may play a role in cognitive performance in older adults.
Deciphering the aetiology of a mixed fungal infection by broad‐range PCR with sequencing and fluorescence in situ hybridisation
Authors: Rickerts V. , McCormick Smith I. , Mousset S. , Kommedal O. , Fredricks D. N.
Published: April 2013

Simultaneous infections with multiple fungi may be misinterpreted as monomicrobial infections by current diagnostics with ramifications for the choice of antimicrobial agents that may impact patient outcomes. The application of molecular methods on tissue samples may be useful to decipher the aetiology of mixed fungal infections. We present a leukaemic patient who died from sepsis due to candidaemia. The postmortem examination documented fungal elements in lung tissue. Fungal DNA was amplified from the lung sample by broad‐range PCR assays targeting the 28S ribosomal RNA gene or the internal transcribed spacer 2 (ITS‐2). Fluorescence in situ hybridisation (FISH) using differentially labelled fungal probes was applied on the tissue. Sequencing identified the PCR amplicons as Aspergillus fumigatus (28S assay) and Candida tropicalis (ITS‐2 assay). As a chromatogram suggested mixed amplicons, the Isentio ripseq® tool for in silico analysis was applied and confirmed the presence of both amplicons in the PCR products of both assays. FISH confirmed the presence of Aspergillus and Candida within the infectious process, a prerequisite for inferring a causal relationship with the infection. The combination of broad‐range PCR with sequence analysis and FISH applied on tissue samples is a powerful approach to identify the aetiology of invasive fungal infections, including mixed infections.
Osteopontin gene SNPs (rs9138, rs11730582) mediate susceptibility to external root resorption in orthodontic patients
Authors: Iglesias‐Linares A , Yañez‐Vico RM , Moreno‐Fernández AM , Mendoza‐Mendoza A , Orce‐Romero A , Solano‐Reina E
Published: April 2013

Objective

External apical root resorption (EARR) is a frequent iatrogenic effect of orthodontic treatment. Substantial variability in responses to postorthodontic EARR has been observed among patients even when similar treatment protocols were used. This observation suggests that environmental and/or genetic variations between individuals may confer susceptibility or resistance to developing EARR. The objective of this study is to determine whether variants in the osteopontin gene, an essential mediator in the odontoclast fusion and attachment process, are positively/negatively associated with postorthodontic EARR.

Materials and Methods

Genetic screening of eighty‐seven orthodontic patients was performed for two polymorphisms in the osteopontin gene cluster (rs9138 and rs11730582). Subjects were divided into groups, according to the presence or absence of EARR (>2 mm). Genotype distributions and allelic frequencies were calculated using the chi‐square test. Logistic regression analysis was used to assess the extent to which clinical‐related parameters interfered with the EARR. Odds ratios (OR) and 95% confidence intervals were also calculated.

Results

Data from this study show that subjects heterozygous and homozygous for the most frequent allele of the osteopontin gene at position 89261521 [OR: 0.035 (P = 0.035*) (allele A)] and 89253600 [OR: 0.20 (P = 0.025*) (allele T)], respectively, are protected against postorthodontic EARR. Nevertheless, a highly significant association was found in the comparative analysis of homozygous subjects [2/2 (CC)] for the osteopontin gene (rs9138), resulting in an increased risk of suffering postorthodontic EARR[OR: 4.10; P = 0.045*;CI: 95%]. Subjects who were homozygous [2/2 (CC)] for the osteopontin gene (rs11730582) were more likely, and to a greater extent, to be affected with EARR [OR: 11.68; P < 0.039*;CI: 95%] compared with other genotypes.

Conclusion

Variations in the osteopontin gene (rs9138 and rs11730582) are determinants of a genetic predisposition to suffer EARR secondary to orthodontic treatment.
Psychopathology and the Ability to Do Otherwise
Authors: Pickard Hanna
Published: April 2013

When philosophers want an example of a person who lacks the ability to do otherwise, they turn to psychopathology. Addicts, agoraphobics, kleptomaniacs, neurotics, obsessives, and even psychopathic serial murderers, are all purportedly subject to irresistible desires that compel the person to act: no alternative possibility is supposed to exist. I argue that this conception of psychopathology is false and offer an empirically and clinically informed understanding of disorders of agency which preserves the ability to do otherwise. First, I appeal to standard clinical treatment for disorders of agency and argue that it undermines this conception of psychopathology. Second, I offer a detailed discussion of addiction, where our knowledge of the neurobiological mechanisms underpinning the disorder is relatively advanced. I argue that neurobiology notwithstanding, addiction is not a form of compulsion and I explain how addiction can impair behavioural control without extinguishing it. Third, I step back from addiction, and briefly sketch what the philosophical landscape more generally looks like without psychopathological compulsion: we lose our standard purported real‐world example of psychologically determined action. I conclude by reflecting on the centrality of choice and free will to our concept of action, and their potency within clinical treatment for disorders of agency.
Multicylinder Flow-Induced Motions: Enhancement by Passive Turbulence Control at 28,000<Re<120,000
Authors: Kim Eun Soo , Bernitsas Michael M. , Ajith Kumar R.
Published: April 2013

The VIVACE converter was introduced at OMAE2006 as a single, smooth, circular-cylinder module. The hydrodynamics of VIVACE is being improved continuously to achieve higher density in harnessed hydrokinetic power. Intercylinder spacing and passive turbulence control (PTC) through selectively located roughness are effective tools in enhancement of flow induced motions (FIMs) under high damping for power harnessing. Single cylinders harness energy at high density even in 1 knot currents. For downstream cylinders, questions were raised on energy availability and sustainability of high-amplitude FIM. Through PTC and intercylinder spacing, strongly synergetic FIMs of 2/3/4 cylinders are achieved. Two-cylinder smooth/PTC, and three/four-cylinder PTC systems are tested experimentally. Using the “PTC-to-FIM” map developed in previous work at the Marine Renewable Energy Laboratory (MRELab), PTC is applied and cylinder response is measured for inflow center-to-center distance 2D-5D (D = diameter), transverse center-to-center distance 0.5–1.5 D, Re ε [28,000–120,000], m* ε [1.677–1.690], U ε [0.36–1.45 m/s], aspect ratio l/D = 10.29, and m*ζ ε [0.0283–0.0346]. All experiments are conducted in the low turbulence free surface water (LTFSW) channel of MRELab. Amplitude spectra and broad field-of-view (FOV) visualization help reveal complex flow structures and cylinder interference undergoing VIV, interference/ proximity/wake/soft/hard galloping. FIM amplitudes of 2.2–2.8D are achieved for all cylinders in steady flow for all parameter ranges tested.
Behavior of a Pontoon Supported by a Mooring Dolphin in a Tsunami (First Report)
Authors: Masuda Mitsuhiro , Masuda Koichi , Ikoma Tomoki , Shoji Kuniaki
Published: April 2013

In recent years, a number of floating facilities for the utilization of ocean space, such as a marine disaster prevention base, floating restaurant, or floating container terminal, are planned, and some of them are actually built. Most of these facilities are of the pontoon-type floating structure, and the mooring system is basically a mooring dolphin. In the design of such facilities, it is important that the prediction of the motions of a pontoon-type floating body, supported by a mooring dolphin, in a tsunami is obtained. The objective of the present research is to develop a simulation system to obtain such predictions. In the present simulation system developed here, the three-dimensional (3D) MPS method (moving particle semi-implicit method) is used, and a solitary wave and borelike wave are applied to represent the incoming tsunami wave. The present paper is a report of the first stage of the research, and the heaving motion of the floating body acted upon by the tsunami is paid special attention, and we also report on the results of the study of the detaching of the floating body from the mooring dolphin.
Low-temperature CVD of η-Mn3N2−x from bis[di(tert-butyl)amido]manganese(II) and ammonia
Authors: Spicer Teresa S. , Spicer Charles W. , Cloud Andrew N. , Davis Luke M. , Girolami Gregory S. , Abelson John R.
Published: April 2013

Manganese nitride films are grown by low-pressure chemical vapor deposition from the novel precursor bis[di(tert-butyl)amido]manganese(II) and ammonia. Mixed-phase films containing crystalline manganese nitride can be grown on substrates at temperatures as low as 80 °C. Above 200 °C, the films consist entirely of crystalline manganese nitride. The crystalline material has the same tetragonal unit cell as η-Mn3N2, but composition analysis of the Mn:N suggests that the material is best denoted as η-Mn3N2−x with x ∼ 0.7. Both oxygen and carbon contamination in the bulk of the films are <1 at. %. Deposition rates of up to 10 nm/min are observed. The growth of crystalline films of a ceramic material at such low temperatures and high rates is highly unusual. The authors attribute this outcome to the presence of high-moment manganese atoms in mixed valence states and to vacancies in the nitrogen sublattice; both features lower the energies needed to break and reform metal-nitrogen bonds and thus allow the deposited atoms to settle more easily into a low-energy ordered arrangement.
Spatial and Temporal Variation in Enterococcal Abundance and Its Relationship to the Microbial Community in Hawaii Beach Sand and Water
Authors: Cui Henglin , Yang Kun , Pagaling Eulyn , Yan Tao
Published: April 2013

Recent studies have reported high levels of fecal indicator enterococci in marine beach sand. This study aimed to determine the spatial and temporal variation of enterococcal abundance and to evaluate its relationships with microbial community parameters in Hawaii beach sand and water. Sampling at 23 beaches on the Island of Oahu detected higher levels of enterococci in beach foreshore sand than in beach water on a mass unit basis. Subsequent 8-week consecutive samplings at two selected beaches (Waialae and Kualoa) consistently detected significantly higher levels of enterococci in backshore sand than in foreshore/nearshore sand and beach water. Comparison between the abundance of enterococci and the microbial communities showed that enterococci correlated significantly with totalVibrioin all beach zones but less significantly with total bacterial density andEscherichia coli. Samples from the different zones of Waialae beach were sequenced by 16S rRNA gene pyrosequencing to determine the microbial community structure and diversity. The backshore sand had a significantly more diverse community and contained different major bacterial populations than the other beach zones, which corresponded to the spatial distribution pattern of enterococcal abundance. Taken together, multiple lines of evidence support the possibility of enterococci as autochthonous members of the microbial community in Hawaii beach sand.
Genetic Diversity and Geographical Distribution of Indigenous Soybean-Nodulating Bradyrhizobia in the United States
Authors: Shiro Sokichi , Matsuura Syota , Saiki Rina , Sigua Gilbert C. , Yamamoto Akihiro , Umehara Yosuke , Hayashi Masaki , Saeki Yuichi
Published: April 2013

We investigated the relationship between the genetic diversity of indigenous soybean-nodulating bradyrhizobia and their geographical distribution in the United States using nine soil isolates from eight states. The bradyrhizobia were inoculated on three soybean
Rj
genotypes (non-
Rj
,
Rj
2
Rj
3
, and
Rj
4
). We analyzed their genetic diversity and community structure by means of restriction fragment length polymorphisms of PCR amplicons to target the 16S-23S rRNA gene internal transcribed spacer region, using 11 USDA
Bradyrhizobium
strains as reference strains. We also performed diversity analysis, multidimensional scaling analysis based on the Bray-Curtis index, and polar ordination analysis to describe the structure and geographical distribution of the soybean-nodulating bradyrhizobial community. The major clusters were
Bradyrhizobium japonicum
Bj123, in the northern United States, and
Bradyrhizobium elkanii
, in the middle to southern regions. Dominance of bradyrhizobia in a community was generally larger for the cluster belonging to
B. elkanii
than for the cluster belonging to
B. japonicum
. The indigenous American soybean-nodulating bradyrhizobial community structure was strongly correlated with latitude. Our results suggest that this community varies geographically.
Simultaneous Catabolism of Plant-Derived Aromatic Compounds Results in Enhanced Growth for Members of the Roseobacter Lineage
Authors: Gulvik Christopher A. , Buchan Alison
Published: April 2013

Plant-derived aromatic compounds are important components of the dissolved organic carbon pool in coastal salt marshes, and their mineralization by resident bacteria contributes to carbon cycling in these systems. Members of the roseobacter lineage of marine bacteria are abundant in coastal salt marshes, and several characterized strains, including
Sagittula stellata
E-37, utilize aromatic compounds as primary growth substrates. The genome sequence of
S. stellata
contains multiple, potentially competing, aerobic ring-cleaving pathways. Preferential hierarchies in substrate utilization and complex transcriptional regulation have been demonstrated to be the norm in many soil bacteria that also contain multiple ring-cleaving pathways. The purpose of this study was to ascertain whether substrate preference exists in
S. stellata
when the organism is provided a mixture of aromatic compounds that proceed through different ring-cleaving pathways. We focused on the protocatechuate (
pca
) and the aerobic benzoyl coenzyme A (
box
) pathways and the substrates known to proceed through them,
p
-hydroxybenzoate (POB) and benzoate, respectively. When these two substrates were provided at nonlimiting carbon concentrations, temporal patterns of cell density, gene transcript abundance, enzyme activity, and substrate concentrations indicated that
S. stellata
simultaneously catabolized both substrates. Furthermore, enhanced growth rates were observed when
S. stellata
was provided both compounds simultaneously compared to the rates of cells grown singly with an equimolar concentration of either substrate alone. This simultaneous-catabolism phenotype was also demonstrated in another lineage member,
Ruegeria pomeroyi
DSS-3. These findings challenge the paradigm of sequential aromatic catabolism reported for soil bacteria and contribute to the growing body of physiological evidence demonstrating the metabolic versatility of roseobacters.
Comparison of 26 Sphingomonad Genomes Reveals Diverse Environmental Adaptations and Biodegradative Capabilities
Authors: Aylward Frank O. , McDonald Bradon R. , Adams Sandra M. , Valenzuela Alejandra , Schmidt Rebeccah A. , Goodwin Lynne A. , Woyke Tanja , Currie Cameron R. , Suen Garret , Poulsen Michael
Published: April 2013

Sphingomonads comprise a physiologically versatile group within the
Alphaproteobacteria
that includes strains of interest for biotechnology, human health, and environmental nutrient cycling. In this study, we compared 26 sphingomonad genome sequences to gain insight into their ecology, metabolic versatility, and environmental adaptations. Our multilocus phylogenetic and average amino acid identity (AAI) analyses confirm that
Sphingomonas
,
Sphingobium
,
Sphingopyxis
, and
Novosphingobium
are well-resolved monophyletic groups with the exception of
Sphingomonas
sp. strain SKA58, which we propose belongs to the genus
Sphingobium
. Our pan-genomic analysis of sphingomonads reveals numerous species-specific open reading frames (ORFs) but few signatures of genus-specific cores. The organization and coding potential of the sphingomonad genomes appear to be highly variable, and plasmid-mediated gene transfer and chromosome-plasmid recombination, together with prophage- and transposon-mediated rearrangements, appear to play prominent roles in the genome evolution of this group. We find that many of the sphingomonad genomes encode numerous oxygenases and glycoside hydrolases, which are likely responsible for their ability to degrade various recalcitrant aromatic compounds and polysaccharides, respectively. Many of these enzymes are encoded on megaplasmids, suggesting that they may be readily transferred between species. We also identified enzymes putatively used for the catabolism of sulfonate and nitroaromatic compounds in many of the genomes, suggesting that plant-based compounds or chemical contaminants may be sources of nitrogen and sulfur. Many of these sphingomonads appear to be adapted to oligotrophic environments, but several contain genomic features indicative of host associations. Our work provides a basis for understanding the ecological strategies employed by sphingomonads and their role in environmental nutrient cycling.
Differentiation of Bacillus anthracis, B. cereus, and B. thuringiensis on the Basis of the
csaB
Gene Reflects Host Source
Authors: Zheng Jinshui , Peng Donghai , Song Xiaoling , Ruan Lifang , Mahillon Jacques , Sun Ming
Published: April 2013

csaB
gene analysis clustered 198 strains of
Bacillus anthracis
,
Bacillus cereus
, and
Bacillus thuringiensis
into two groups related to mammalian and insect hosts, respectively. Mammal-related group I strains also have more S-layer homology (SLH) protein genes than group II strains. This indicates that
csaB
-based differentiation reflects selective pressure from animal hosts.
Alternative Sigma Factor SigK Has a Role in Stress Tolerance of Group I Clostridium botulinum Strain ATCC 3502
Authors: Dahlsten Elias , Kirk David , Lindstrï¿½m Miia , Korkeala Hannu
Published: April 2013

The role of the alternative sigma factor SigK in cold and osmotic stress tolerance of
Clostridium botulinum
ATCC 3502 was demonstrated by induction of
sigK
after temperature downshift and exposure to hyperosmotic conditions and by impaired growth of the
sigK
mutants under the respective conditions.
Comparative Transcriptomics of Infectious Spores from the Fungal Pathogen Histoplasma capsulatum Reveals a Core Set of Transcripts That Specify Infectious and Pathogenic States
Authors: Inglis Diane O. , Voorhies Mark , Hocking Murray Davina R. , Sil Anita
Published: April 2013

Histoplasma capsulatum
is a fungal pathogen that infects both healthy and immunocompromised hosts. In regions where it is endemic,
H. capsulatum
grows in the soil and causes respiratory and systemic disease when inhaled by humans. An interesting aspect of
H. capsulatum
biology is that it adopts specialized developmental programs in response to its environment. In the soil, it grows as filamentous chains of cells (mycelia) that produce asexual spores (conidia). When the soil is disrupted, conidia aerosolize and are inhaled by mammalian hosts. Inside a host, conidia germinate into yeast-form cells that colonize immune cells and cause disease. Despite the ability of conidia to initiate infection and disease, they have not been explored on a molecular level. We developed methods to purify
H. capsulatum
conidia, and we show here that these cells germinate into filaments at room temperature and into yeast-form cells at 37°C. Conidia internalized by macrophages germinate into the yeast form and proliferate within macrophages, ultimately lysing the host cells. Similarly, infection of mice with purified conidia is sufficient to establish infection and yield viable yeast-form cells
in vivo
. To characterize conidia on a molecular level, we performed whole-genome expression profiling of conidia, yeast, and mycelia from two highly divergent
H. capsulatum
strains. In parallel, we used homology and protein domain analysis to manually annotate the predicted genes of both strains. Analyses of the resultant data defined sets of transcripts that reflect the unique molecular states of
H. capsulatum
conidia, yeast, and mycelia.
Pbp1 Is Involved in Ccr4- and Khd1-Mediated Regulation of Cell Growth through Association with Ribosomal Proteins Rpl12a and Rpl12b
Authors: Kimura Yuichi , Irie Kaoru , Irie Kenji
Published: April 2013

The
Saccharomyces cerevisiae
Pbp1 [poly(A)-binding protein (Pab1)-binding protein] is believed to be involved in RNA metabolism and regulation of translation, since Pbp1 regulates a length of poly(A) tail and is involved in stress granule (SG) formation. However, a physiological function of Pbp1 remains unclear, since the
pbp1
Δ mutation has no obvious effect on cell growth. In this study, we showed that
PBP1
genetically interacts with
CCR4
and
KHD1
, which encode a cytoplasmic deadenylase and an RNA-binding protein, respectively. Ccr4 and Khd1 modulate a signal from Rho1 in the cell wall integrity pathway by regulating the expression of RhoGEF and RhoGAP, and the double deletion of
CCR4
and
KHD1
confers a severe growth defect displaying cell lysis. We found that the
pbp1
Δ mutation suppressed the growth defect caused by the
ccr4Δ khd1
Δ mutation. The
pbp1
Δ mutation also suppressed the growth defect caused by double deletion of
POP2
, encoding another cytoplasmic deadenylase, and
KHD1
. Deletion of the gene encoding previously known Pbp1-interacting factor Lsm12, Pbp4, or Mkt1 did not suppress the growth defect of the
ccr4Δ khd1
Δ mutant, suggesting that Pbp1 acts independently of these factors in this process. We then screened novel Pbp1-interacting factors and found that Pbp1 interacts with ribosomal proteins Rpl12a and Rpl12b. Similarly to the
pbp1
Δ mutation, the
rpl12a
Δ and
rpl12b
Δ mutations also suppressed the growth defect caused by the
ccr4Δ khd1
Δ mutation. Our results suggest that Pbp1 is involved in the Ccr4- and Khd1-mediated regulation of cell growth through the association with Rpl12a and Rpl12b.
Endogenous Mutagenesis in Recombinant Sulfolobus Plasmids
Authors: Sakofsky Cynthia J. , Grogan Dennis W.
Published: April 2013

Low rates of replication errors in chromosomal genes of
Sulfolobus
spp. demonstrate that these extreme thermoacidophiles can maintain genome integrity in environments with high temperature and low pH. In contrast to this genetic stability, we observed unusually frequent mutation of the β-
d
-glycosidase gene (
lacS
) of a shuttle plasmid (pJ
lacS
) propagated in
Sulfolobus acidocaldarius
. The resulting Lac
−
mutants also grew faster than the Lac
+
parent, thereby amplifying the impact of the frequent
lacS
mutations on the population. We developed a mutant accumulation assay and corrections for the effects of copy number and differential growth for this system; the resulting measurements and calculations yielded a corrected rate of 5.1 × 10
−4
mutational events at the
lacS
gene per plasmid replication. Analysis of independent
lacS
mutants revealed three types of mutations: (i) G·C-to-A·T transitions, (ii) slipped-strand events, and (iii) deletions. These mutations were frequent in plasmid-borne
lacS
expressed at a high level but not in single-copy
lacS
in the chromosome or at lower levels of expression in a plasmid. Substitution mutations arose at only two of 12 potential priming sites of the DNA primase of the pRN1 replicon, but nearly all these mutations created nonsense (chain termination) codons. The spontaneous mutation rate of plasmid-borne
lacS
was 175-fold higher under high-expression than under low-expression conditions. The results suggest that important DNA repair or replication fidelity functions are impaired or overwhelmed in pJ
lacS
, with results analogous to those of the “transcription-associated mutagenesis” seen in bacteria and eukaryotes.
Secretion of TcpF by the Vibrio cholerae Toxin-Coregulated Pilus Biogenesis Apparatus Requires an N-Terminal Determinant
Authors: Megli Christina J. , Taylor Ronald K.
Published: April 2013

Type IV pili are important for microcolony formation, biofilm formation, twitching motility, and attachment. We and others have shown that type IV pili are important for protein secretion across the outer membrane, similar to type II secretion systems. This study explored the relationship between protein secretion and pilus formation in
Vibrio cholerae
. The toxin-coregulated pilus (TCP), a type IV pilus required for
V. cholerae
pathogenesis, is necessary for the secretion of the colonization factor TcpF (T. J. Kirn, N. Bose, and R. K. Taylor, Mol. Microbiol.
49:
81–92, 2003). This phenomenon is not unique to
V. cholerae
; secreted virulence factors that are dependent on the presence of components of the type IV pilus biogenesis apparatus for secretion have been reported with
Dichelobacter nodosus
(R. M. Kennan, O. P. Dhungyel, R. J. Whittington, J. R. Egerton, and J. I. Rood, J. Bacteriol.
183:
4451–4458, 2001) and
Francisella tularensis
(A. J. Hager et al., Mol. Microbiol.
62:
227–237, 2006). Using site-directed mutagenesis, we demonstrated that the secretion of TcpF is dependent on the presence of selected amino acid R groups at position five. We were unable to find other secretion determinants, suggesting that Y5 is the major secretion determinant within TcpF. We also report that proteins secreted in a type IV pilus biogenesis apparatus-dependent manner have a YXS motif within the first 15 amino acids following the Sec cleavage site. The YXS motif is not present in proteins secreted by type II secretion systems, indicating that this is unique to type IV pilus-mediated secretion. Moreover, we show that TcpF interacts with the pilin TcpA, suggesting that these proteins are secreted by the type IV pilus biogenesis system. These data provide a starting point for understanding how type IV pili can mediate secretion of virulence factors important for bacterial pathogenesis.
The Bartonella quintana Extracytoplasmic Function Sigma Factor RpoE Has a Role in Bacterial Adaptation to the Arthropod Vector Environment
Authors: Abromaitis Stephanie , Koehler Jane E.
Published: April 2013

Bartonella quintana
is a vector-borne bacterial pathogen that causes fatal disease in humans. During the infectious cycle,
B. quintana
transitions from the hemin-restricted human bloodstream to the hemin-rich body louse vector. Because extracytoplasmic function (ECF) sigma factors often regulate adaptation to environmental changes, we hypothesized that a previously unstudied
B. quintana
ECF sigma factor, RpoE, is involved in the transition from the human host to the body louse vector. The genomic context of
B. quintana
rpoE
identified it as a member of the ECF15 family of sigma factors found only in alphaproteobacteria. ECF15 sigma factors are believed to be the master regulators of the general stress response in alphaproteobacteria. In this study, we examined the
B. quintana
RpoE response to two stressors that are encountered in the body louse vector environment, a decreased temperature and an increased hemin concentration. We determined that the expression of
rpoE
is significantly upregulated at the body louse (28°C) versus the human host (37°C) temperature.
rpoE
expression also was upregulated when
B. quintana
was exposed to high hemin concentrations.
In vitro
and
in vivo
analyses demonstrated that RpoE function is regulated by a mechanism involving the anti-sigma factor NepR and the response regulator PhyR. The Δ
rpoE
Δ
nepR
mutant strain of
B. quintana
established that RpoE-mediated transcription is important in mediating the tolerance of
B. quintana
to high hemin concentrations. We present the first analysis of an ECF15 sigma factor in a vector-borne human pathogen and conclude that RpoE has a role in the adaptation of
B. quintana
to the hemin-rich arthropod vector environment.
Characterization of an
ntrX
Mutant of Neisseria gonorrhoeae Reveals a Response Regulator That Controls Expression of Respiratory Enzymes in Oxidase-Positive Proteobacteria
Authors: Atack John M. , Srikhanta Yogitha N. , Djoko Karrera Y. , Welch Jessica P. , Hasri Norain H. M. , Steichen Christopher T. , Vanden Hoven Rachel N. , Grimmond Sean M. , Othman Dk Seti Maimonah Pg , Kappler Ulrike , Apicella Michael A. , Jennings Michael P. , Edwards Jennifer L. , McEwan Alastair G.
Published: April 2013

NtrYX is a sensor-histidine kinase/response regulator two-component system that has had limited characterization in a small number of
Alphaproteobacteria
. Phylogenetic analysis of the response regulator NtrX showed that this two-component system is extensively distributed across the bacterial domain, and it is present in a variety of
Betaproteobacteria
, including the human pathogen
Neisseria gonorrhoeae
. Microarray analysis revealed that the expression of several components of the respiratory chain was reduced in an
N. gonorrhoeae
ntrX
mutant compared to that in the isogenic wild-type (WT) strain 1291. These included the cytochrome
c
oxidase subunit (
ccoP
), nitrite reductase (
aniA
), and nitric oxide reductase (
norB
). Enzyme activity assays showed decreased cytochrome oxidase and nitrite reductase activities in the
ntrX
mutant, consistent with microarray data.
N. gonorrhoeae
ntrX
mutants had reduced capacity to survive inside primary cervical cells compared to the wild type, and although they retained the ability to form a biofilm, they exhibited reduced survival within the biofilm compared to wild-type cells, as indicated by LIVE/DEAD staining. Analyses of an
ntrX
mutant in a representative alphaproteobacterium,
Rhodobacter capsulatus
, showed that cytochrome oxidase activity was also reduced compared to that in the wild-type strain SB1003. Taken together, these data provide evidence that the NtrYX two-component system may be a key regulator in the expression of respiratory enzymes and, in particular, cytochrome
c
oxidase, across a wide range of proteobacteria, including a variety of bacterial pathogens.
Biochemical and Structural Studies of the Mycobacterium tuberculosis
O
6
-Methylguanine Methyltransferase and Mutated Variants
Authors: Miggiano Riccardo , Casazza Valentina , Garavaglia Silvia , Ciaramella Maria , Perugino Giuseppe , Rizzi Menico , Rossi Franca
Published: April 2013

Mycobacterium tuberculosis
displays remarkable genetic stability despite continuous exposure to the hostile environment represented by the host's infected macrophages. Similarly to other organisms,
M. tuberculosis
possesses multiple systems to counteract the harmful potential of DNA alkylation. In particular, the suicidal enzyme
O
6
-methylguanine-DNA methyltransferase (OGT) is responsible for the direct repair of
O
6
-alkylguanine in double-stranded DNA and is therefore supposed to play a central role in protecting the mycobacterial genome from the risk of G·C-to-A·T transition mutations. Notably, a number of geographically widely distributed
M. tuberculosis
strains shows nonsynonymous single-nucleotide polymorphisms in their OGT-encoding gene, leading to amino acid substitutions at position 15 (T15S) or position 37 (R37L) of the N-terminal domain of the corresponding protein. However, the role of these mutations in
M. tuberculosis
pathogenesis is unknown. We describe here the
in vitro
characterization of
M. tuberculosis
OGT (
Mt
OGT) and of two point-mutated versions of the protein mimicking the naturally occurring ones, revealing that both mutated proteins are impaired in their activity as a consequence of their lower affinity for alkylated DNA than the wild-type protein. The analysis of the crystal structures of
Mt
OGT and
Mt
OGT-R37L confirms the high level of structural conservation of members of this protein family and provides clues to an understanding of the molecular bases for the reduced affinity for the natural substrate displayed by mutated
Mt
OGT. Our
in vitro
results could contribute to validate the inferred participation of mutated OGTs in
M. tuberculosis
phylogeny and biology.
Missed diagnosis of a gallstone ileus: an incomplete laparoscopy due to a putative ventriculoperitoneal shunt infection
Authors: Däster Silvio , Nebiker Christian A , Hohmann Joachim , Droeser Raoul A
Published: April 2013

A 90-year-old woman presented with abdominal pain and vomiting. Initial investigations revealed diffuse abdominal tenderness and fever, combined with leucocytosis and marked elevation of C reactive protein levels. Abdominal CT demonstrated segmental bowel wall thickening in the jejunum near the tip of a ventriculoperitoneal (VP) shunt, which had been placed 17 years before because of hydrocephalus. Pneumobilia was present but no ectopic gallstone was detected at the initial analysis and there were no signs of mechanical ileus. Immediate laparoscopy was performed to exclude small bowel ischaemia. Owing to purulent ascites the VP shunt was externalised, supposing VP shunt infection with reactive jejunitis to be the main problem. Antibiotic treatment was then administered and the remaining part of the shunt was removed 6 days later. However, clinical signs of intestinal obstruction have been aggravated. Therefore, a laparoscopy was repeated 3 days later and a gallstone ileus was diagnosed. After enterolithotomy through a minilaparotomy, the patient was fully recovered.
Acute hepatitis in a young woman with systemic lupus erythematosus: a diagnostic challenge
Authors: Barosa Rita , Ramos Lídia Roque , Fonseca Cristina , Freitas João
Published: April 2013

A 48-year-old woman with systemic lupus erythematosus diagnosis was on naproxen, hidroxichloroquine and acetylsalicylic acid. She had self-suspended all medication and resumed 1 year later. Five days after the medication was resumed, she developed acute hepatitis, with biochemical hepatic cytolysis, hypergamaglobulinaemia and a serum antinuclear antibody titre of 1/2560. Idiopathic autoimmune hepatitis was considered, but drug-induced liver injury could not definitely be ruled out. Patient declined liver biopsy. Oral prednisolone was started. Within 3 months with prednisolone being tapered to 10 mg/day, a new flare occurred. Liver biopsy was performed and it favoured autoimmune hepatitis diagnosis. We discuss the diagnostic options and treatment approach in a patient with autoimmune disease and possible drug-induced liver injury who initially declined liver biopsy.
Spontaneous bacterial peritonitis by Brucella in a cirrhotic patient
Authors: Ferreira Alexandre Oliveira , Martins Luis Nogueira , Marinho Rui Tato , Velosa José
Published: April 2013

Spontaneous bacterial peritonitis (SBP) is a frequent form of decompensation of end-stage liver disease, with an incidence of 15–20% and a short-term mortality of 10–33%. The usual causative agents (90% of SBP) are enteric Gram-negative bacteria—Escherichia coliandKlebsiella pneumoniae. Brucella is known to be a possible, but exceedingly rare, causative agent of SBP. We present the case of a 47-year-old Egyptian man, with hepatitis C cirrhosis, and a 2 week history of ascites, jaundice, encephalopathy, fever and pain on his right shoulder that started while travelling in the Middle East. Laboratory and imaging studies were undertaken and he was diagnosed an SBP that failed to respond to Imipenem. Brucella was identified both in the ascitic fluid and blood; he was started on doxycycline plus rifampin with immediate clinical improvement. The antibiotic regimen was kept for 8 weeks. The patient is currently under evaluation for liver transplantation.
Prematurity, macrosomia, hyperinsulinaemic hypoglycaemia and a dominantABCC8gene mutation
Authors: Khoriati Dana , Arya Ved Bhushan , Flanagan Sarah E , Ellard Sian , Hussain Khalid
Published: April 2013

Congenital hyperinsulinism (CHI) is a rare cause of hyperinsulinaemic hypoglycaemia (HH) and is due to an inappropriate secretion of insulin by the pancreatic β-cells. Genetic defects in key genes lead to dysregulated insulin secretion and consequent hypoglycaemia. Mutations in the genesABCC8/KCNJ11, encoding SUR1/Kir6.2 components of the KATPchannels, respectively, are the commonest cause of CHI. A 33+6 week gestation male infant weighing 3.38 kg (above 90th centile) presented with severe neonatal symptomatic hypoglycaemia. He required a glucose infusion rate of 20 mg/kg/min to maintain normoglycaemia (blood glucose levels at >3.5 mmol/l). Investigations established the diagnosis of HH (blood glucose 2.2 mmol/l with simultaneous insulin of 97.4 mU/l). Subsequent molecular genetic studies identified a heterozygous pathogenicABCC8missense mutation, p.R1353H (c.4058G>A), inherited from an unaffected mother. His HH was diazoxide responsive and resolved within 3 months of life.
GENERALIZED THREE-PARTY QUBIT OPERATION SHARING
Authors: LIU DAOCHU , LIU YIMIN , YIN XIAOFENG , LIU XIANSONG , ZHANG ZHANJUN
Published: April 2013

Two three-party schemes of qubit operation sharing proposed by Zhang and Cheung [J. Phys. B44 (2011) 165508] are generalized by utilizing partially entangled states as quantum channels instead of maximally entangled ones. Their quantum and classical resource consumptions, necessary-operation complexities, success probabilities and efficiencies are calculated and compared with each other. Moreover, it is revealed that the success probabilities are completely determined by the shared entanglement.
THE INFLUENCE OF DEBORAH NUMBER ON SOME COUETTE FLOWS OF A MAXWELL FLUID
Authors: SHAHID NAZISH , RANA MEHWISH
Published: April 2013

Some Couette flows of a Maxwell fluid caused by the bottom plate applying shear rate on the fluid, are studied. Exact expressions for velocity and shear stress corresponding to the fluid motion are determined using Laplace transform. Two particular cases of constant shear rate on the bottom plate and sinusoidal oscillations of the wall shear rate are discussed. Some important characteristics of fluid motion are highlighted through graphs.