bluuebunny/crossref_metadata_2025 huggingface dataset:
Heavy Axle Load Revenue Service Bridge Approach Problems and Remedies
Authors: Li Dingqing , Maal Luis
Published: June 2015

Two different remedies to reduce track stiffness and increase track damping for the track on the bridges were implemented for two separate ballast deck bridges with standard concrete ties located on a high tonnage heavy haul revenue service route. One remedy used concrete ties fitted with rubber pads on the bottom surface and the other used ballast mats between the ballast layer and bridge deck. The ballast sections were increased to a minimum depth of 12 inches below the bottom of the ties, and drainage improvement was made to ensure that water would not accumulate on the bridges or in the approaches.

The two bridge locations were selected in September 2007 and June 2009, for remediation and long-term monitoring of performance as part of the heavy axle load revenue service mega site testing program conducted by Transportation Technology Center, Inc. and Union Pacific Railroad.

Before remediation, these two locations experienced excessive track geometry degradation, mud pumping, and track component failure that required localized maintenance work on a quarterly basis (approximately 63 MGT).

After remediation, no localized maintenance (except yearly surfacing operations for the entire line) has been required for more than 1,000 MGT.

The main root causes of these problems were determined to be high track stiffness and low track damping for the track on the bridges, which adversely affected dynamic vehicle-track interaction when differential track settlement started to occur at the bridge approaches. Some of these ballast deck bridges with concrete ties had track modulus measured at 12,000 lb/in/in, which is considered too high to accommodate dynamic vehicle-track interaction.

Long-term performance of these remedies has been excellent, resulting in significant benefits from reduction of slow orders, train delays, and major track maintenance activities.
A Review of Past Geotechnical Performance of the Hudson Bay Rail Embankment and Its Comparison to the Current Condition
Authors: Addison Priscilla E. , Oommen Thomas , Lautala Pasi
Published: June 2015

The Hudson Bay Railway (HBR) is a 510 mile railway completed in 1929 in northern Manitoba, Canada. It connects domestic locations in North America with international destinations through the Port of Churchill.

Permafrost was encountered during construction at milepost 136 in isolated peat bogs which continued in a gradual northward transition from discontinuous to continuous permafrost. Over the past 80 years, warming climate combined with poor engineering properties of the railway embankment material has resulted in further thawing of the discontinuous permafrost leading to differential settlement along the rail embankment and high annual maintenance costs.

In a bid to understand the geothermal regime of the embankment, underlying subsurface condition, and to seek for solutions to stabilize the embankment, extensive work has been done from 1977 to the present time. This paper seeks to review reports of the past projects and compare the results against current conditions at selected test locations.
Identifying Electrically Infeasible Traffic Scenarios on the Iron Ore Line; Applied on the Present-Day System, Converter Station Outages, and Optimal Locomotive Reactive Power Strategies
Authors: Abrahamsson Lars , Skogberg Ronny , Östlund Stefan , Lagos Mario , Söder Lennart
Published: June 2015

This paper presents the main findings of a Master’s Thesis project carried out in cooperation between Transrail and Royal Institute of Technology (KTH). The main objective was to create a plugin for checking the electric power system feasibility of a train traffic plan with an associated driving strategy created by TRAINS — a Transrail software product. Secondary aims with the project was to study power system feasibilities during converter station outages, and to which extent optimal operation of the locomotive converters’ reactive power assure power system feasibilities.

In the developed optimal reactive power strategies, the main priority was to fulfill the desired traffic plans, whereas the secondary priority was to minimize railway power system power consumption.

The case studies are applied on representative traffic scenarios and power system models representing the northern part of the Iron Ore line in Northern Sweden. The focus of the study is set on the IORE locomotives and the iron ore trains they haul. The optimized locomotive reactive power regards IORE, so also the investigated power system feasibilities of the traffic plans.
A new automated quantification algorithm for the detection and evaluation of focal liver lesions with contrast‐enhanced ultrasound
Authors: Gatos Ilias , Tsantis Stavros , Spiliopoulos Stavros , Skouroliakou Aikaterini , Theotokas Ioannis , Zoumpoulis Pavlos , Hazle John D. , Kagadis George C.
Published: June 2015

Purpose:

Detect and classify focal liver lesions (FLLs) from contrast‐enhanced ultrasound (CEUS) imaging by means of an automated quantification algorithm.

Methods:

The proposed algorithm employs a sophisticated segmentation method to detect and contour focal lesions from 52 CEUS video sequences (30 benign and 22 malignant). Lesion detection involves wavelet transform zero crossings utilization as an initialization step to the Markov random field model toward the lesion contour extraction. After FLL detection across frames, time intensity curve (TIC) is computed which provides the contrast agents’ behavior at all vascular phases with respect to adjacent parenchyma for each patient. From each TIC, eight features were automatically calculated and employed into the support vector machines (SVMs) classification algorithm in the design of the image analysis model.

Results:

With regard to FLLs detection accuracy, all lesions detected had an average overlap value of 0.89 ± 0.16 with manual segmentations for all CEUS frame‐subsets included in the study. Highest classification accuracy from the SVM model was 90.3%, misdiagnosing three benign and two malignant FLLs with sensitivity and specificity values of 93.1% and 86.9%, respectively.

Conclusions:

The proposed quantification system that employs FLLs detection and classification algorithms may be of value to physicians as a second opinion tool for avoiding unnecessary invasive procedures.
Reduced Radial Displacement of the Gastrocnemius Medialis Muscle After Electrically Elicited Fatigue
Authors: Macgregor Lewis J. , Ditroilo Massimiliano , Smith Iain J. , Fairweather Malcolm M. , Hunter Angus M.
Published: June 2015

Context:

Assessments of skeletal-muscle functional capacity often necessitate maximal contractile effort, which exacerbates muscle fatigue or injury. Tensiomyography (TMG) has been investigated as a means to assess muscle contractile function after fatigue; however, observations have not been contextualized by concurrent physiological measures.

Objective:

To measure peripheral-fatigue-induced alterations in mechanical and contractile properties of the plantar-flexor muscles through noninvasive TMG concurrently with maximal voluntary contraction (MVC) and passive muscle tension (PMT) to validate TMG as a gauge of peripheral fatigue.

Design:

Pre- and posttest intervention with control.

Setting:

University laboratory.

Participants:

21 healthy male volunteers.

Interventions:

Subjects’ plantar flexors were tested for TMG parameters, along with MVC and PMT, before and after either a 5-min rest period (control) or a 5-min electrical-stimulation intervention (fatigue).

Main Outcome Measures:

Temporal (contraction velocity) and spatial (radial displacement) contractile parameters of the gastrocnemius medialis were recorded through TMG. MVC was measured as an indicator of muscle fatigue, and PMT was measured to assess muscle stiffness.

Results:

Radial displacement demonstrated a fatigue-associated reduction (3.3 ± 1.2 vs 4.0 ± 1.4 mm, P = .031), while contraction velocity remained unaltered. In addition, MVC significantly declined by 122.6 ± 104 N (P < .001) after stimulation (fatigue). PMT was significantly increased after fatigue (139.8 ± 54.3 vs 111.3 ± 44.6 N, P = .007).

Conclusions:

TMG successfully detected fatigue, evident from reduced MVC, by displaying impaired muscle displacement accompanied by elevated PMT. TMG could be useful in establishing skeletalmuscle fatigue status without exacerbating the functional decrement of the muscle.
Russian foundation tarred with ‘foreign’ label
Authors: Pokrovsky Vladimir
Published: June 2015

Founder may pull plug on private research funder.
Did good genes help people outlast brutal Leningrad siege?
Authors: Smirnova Yulia , Davydova Angelina
Published: June 2015

Study hints at more efficient metabolism in survivors.
The poisoned necklace
Authors: Lawler Andrew
Published: June 2015

In the 1950s, a visit by a single outsider sickened a band of tribespeople.
Mercy on these people, and give us a road
Authors: Lawler Andrew
Published: June 2015

Will a road through the rainforest bring prosperity or disaster?
Response to Comment on “Human-like hand use in
Australopithecus africanus
”
Authors: Skinner Matthew M. , Stephens Nicholas B. , Tsegai Zewdi J. , Foote Alexandra C. , Nguyen N. Huynh , Gross Thomas , Pahr Dieter H. , Hublin Jean-Jacques , Kivell Tracy L.
Published: June 2015

Almécija and colleagues claim that we apply a simplified understanding of bone functional adaptation and that our results of human-like hand use in
Australopithecus africanus
are not novel. We argue that our results speak to actual behavior, rather than potential behaviors, and our functional interpretation is well supported by our methodological approach, comparative sample, and previous experimental data.
Error-prone chromosome-mediated spindle assembly favors chromosome segregation defects in human oocytes
Authors: Holubcová Zuzana , Blayney Martyn , Elder Kay , Schuh Melina
Published: June 2015

Earliest stages of human development revealed

Most of our knowledge about meiosis in mammalian oocytes stems from studies of mouse oocytes. However, chromosome segregation in mouse oocytes is much more reliable than in human oocytes. Working with the clinic that first pioneered IVF, Holubcové
et al.
studied freshly harvested human oocytes. They used high-resolution fluorescence microscopy to watch more than 100 human oocytes as they went through each step of meiosis.

Science
, this issue p.
1143
Exceptional epigenetics in the brain
Authors: Luo Chongyuan , Ecker Joseph R.
Published: June 2015

Non-CG DNA methylation modulates gene expression in the adult brain
A direct screen for c-di-GMP modulators reveals a
Salmonella
Typhimurium periplasmic ʟ-arginine–sensing pathway
Authors: Mills Erez , Petersen Erik , Kulasekara Bridget R. , Miller Samuel I.
Published: June 2015

The human pathogen
Salmonella
senses ʟ-arginine and responds by increasing c-di-GMP and cellulose synthesis.
Driving regeneration in mice
Authors: Smith Orla
Published: June 2015

The capacity for regeneration can be elicited in adult mice by drug-induced stabilization of HIF-1α (hypoxia-inducible factor 1α).
Exosomes prep the metastatic site
Authors: Ferrarelli Leslie K.
Published: June 2015

Pancreatic tumors release exosomes that prime the liver for metastasis.
Genetic variants associated with autoimmunity drive NFκB signaling and responses to inflammatory stimuli
Authors: Housley William J. , Fernandez Salvador D. , Vera Kenneth , Murikinati Sasidhar R. , Grutzendler Jaime , Cuerdon Nicole , Glick Laura , De Jager Phillip L. , Mitrovic Mitja , Cotsapas Chris , Hafler David A.
Published: June 2015

Genetic variants associated with multiple sclerosis result in increased NFκB signaling in CD4 T cells and a decreased threshold for activation.
The slow road to memory loss
Authors: Ju Yo-El
Published: June 2015

β-Amyloid pathology may impair memory function in Alzheimer’s disease and aging by decreasing slow wave activity during sleep.
On the origin of fat fibrosis
Authors: Shaw Tanya J.
Published: June 2015

Perivascular adipocyte progenitors can be tipped to fibrose by growth factor signaling in white adipose tissues.
Timing is everything
Authors: Suzuki Masako
Published: June 2015

Prenatal exposure to famine has a critical time period for DNA-methylation alterations in blood cells later in life.
Incomplete APOBEC3G/F Neutralization by HIV-1 Vif Mutants Facilitates the Genetic Evolution from CCR5 to CXCR4 Usage
Authors: Alteri Claudia , Surdo Matteo , Bellocchi Maria Concetta , Saccomandi Patrizia , Continenza Fabio , Armenia Daniele , Parrotta Lucia , Carioti Luca , Costa Giosuè , Fourati Slim , Di Santo Fabiola , Scutari Rossana , Barbaliscia Silvia , Fedele Valentina , Carta Stefania , Balestra Emanuela , Alcaro Stefano , Marcelin Anne Genevieve , Calvez Vincent , Ceccherini-Silberstein Francesca , Artese Anna , Perno Carlo Federico , Svicher Valentina
Published: June 2015

Incomplete APOBEC3G/F neutralization by a defective HIV-1Vif protein can promote genetic diversification by inducing G-to-A mutations in the HIV-1 genome. The HIV-1 Env V3 loop, critical for coreceptor usage, contains several putative APOBEC3G/F target sites. Here, we determined if APOBEC3G/F, in the presence of Vif-defective HIV-1 virus, can induce G-to-A mutations at V3 positions critical to modulation of CXCR4 usage. Peripheral blood mononuclear cells (PBMC) and monocyte-derived macrophages (MDM) from 2 HIV-1-negative donors were infected with CCR5-using 81.A-VifWTvirus (i.e., with wild-type [WT] Vif protein), 81.A-VifE45G, or 81.A-VifK22E(known to incompletely/partially neutralize APOBEC3G/F). The rate of G-toA mutations was zero or extremely low in 81.A-VifWT- and 81.A-VifE45G-infected PBMC from both donors. Conversely, G-to-A enrichment was detected in 81.A-VifK22E-infected PBMC (prevalence ranging from 2.18% at 7 days postinfection [dpi] to 3.07% at 21 dpi in donor 1 and from 10.49% at 7 dpi to 8.69% at 21 dpi in donor 2). A similar scenario was found in MDM. G-to-A mutations occurred at 8 V3 positions, resulting in nonsynonymous amino acid substitutions. Of them, G24E and E25K strongly correlated with phenotypically/genotypically defined CXCR4-using viruses (P= 0.04 and 5.5e−7, respectively) and increased the CXCR4 N-terminal binding affinity for V3 (WT, −40.1 kcal/mol; G24E, −510 kcal/mol; E25K, −522 kcal/mol). The analysis of paired V3 and Vif DNA sequences from 84 HIV-1-infected patients showed that the presence of a Vif-defective virus correlated with CXCR4 usage in proviral DNA (P= 0.04). In conclusion, incomplete APOBEC3G/F neutralization by a single Vif amino acid substitution seeds a CXCR4-using proviral reservoir. This can have implications for the success of CCR5 antagonist-based therapy, as well as for the risk of disease progression.
Characterization of BKC-1 Class A Carbapenemase from Klebsiella pneumoniae Clinical Isolates in Brazil
Authors: Nicoletti Adriana Giannini , Marcondes Marcelo F. M. , Martins Willames M. B. S. , Almeida Luiz G. P. , Nicolás Marisa F. , Vasconcelos Ana T. R. , Oliveira Vitor , Gales Ana Cristina
Published: June 2015

Three
Klebsiella pneumoniae
clinical isolates demonstrating carbapenem resistance were recovered from different patients hospitalized at two medical centers in São Paulo, Brazil. Resistance to all β-lactams, quinolones, and some aminoglycosides was observed for these isolates that were susceptible to polymyxin B. Carbapenem hydrolysis, which was inhibited by clavulanic acid, was observed for all
K. pneumoniae
isolates that belonged to the same pulsed-field gel electrophoresis (PFGE) type and a novel sequence type (ST), ST1781 (clonal complex 442 [CC442]). A 10-kb nonconjugative incompatibility group Q (IncQ) plasmid, denominated p60136, was transferred to
Escherichia coli
strain TOP10 cells by electroporation. The full sequencing of p60136 showed that it was composed of a mobilization system, IS
Kpn23
, the phosphotransferase aph3A-VI, and a 941-bp open reading frame (ORF) that codified a 313-amino acid protein. This ORF was named
bla
BKC-1
. Brazilian
Klebsiella
carbapenemase-1 (BKC-1) showed a pI of 6.0 and possessed the highest identity (63%) with a β-lactamase of
Sinorhizobium meliloti
, an environmental bacterium. Hydrolysis studies demonstrated that purified BKC-1 not only hydrolyzed carbapenems but also penicillins, cephalosporins, and monobactams. However, the carbapenems were less efficiently hydrolyzed due to their very low

k
cat

values (0.0016 to 0.031 s
−1
). In fact, oxacillin was the best substrate for BKC-1 (

k
cat

/

K
m

, 53,522.6 mM
−1
s
−1
). Here, we report a new class A carbapenemase, confirming the diversity and rapid evolution of β-lactamases in
K. pneumoniae
clinical isolates.
Calcium-Mediated Induction of Paradoxical Growth following Caspofungin Treatment Is Associated with Calcineurin Activation and Phosphorylation in Aspergillus fumigatus
Authors: Juvvadi Praveen R. , Muñoz Alberto , Lamoth Frédéric , Soderblom Erik J. , Moseley M. Arthur , Read Nick D. , Steinbach William J.
Published: June 2015

The echinocandin antifungal drug caspofungin at high concentrations reverses the growth inhibition of
Aspergillus fumigatus
, a phenomenon known as the “paradoxical effect,” which is not consistently observed with other echinocandins (micafungin and anidulafungin). Previous studies of
A. fumigatus
revealed the loss of the paradoxical effect following pharmacological or genetic inhibition of calcineurin, yet the underlying mechanism is poorly understood. Here, we utilized a codon-optimized bioluminescent Ca
2+
reporter aequorin expression system in
A. fumigatus
and showed that caspofungin elicits a transient increase in cytosolic free Ca
2+
([Ca
2+
]
c
) in the fungus that acts as the initial trigger of the paradoxical effect by activating calmodulin-calcineurin signaling. While the increase in [Ca
2+
]
c
was also observed upon treatment with micafungin, another echinocandin without the paradoxical effect, a higher [Ca
2+
]
c
increase was noted with the paradoxical-growth concentration of caspofungin. Treatments with a Ca
2+
-selective chelator, BAPTA [1,2-bis(
o
-aminophenoxy)ethane-
N
,
N
,
N
′,
N
′-tetraacetic acid], or the L-type Ca
2+
channel blocker verapamil abolished caspofungin-mediated paradoxical growth in both the wild-type and the echinocandin-resistant (EMFR-S678P) strains. Concomitant with increased [Ca
2+
]
c
levels at higher concentrations of caspofungin, calmodulin and calcineurin gene expression was enhanced. Phosphoproteomic analysis revealed that calcineurin is activated through phosphorylation at its serine-proline-rich region (SPRR), a domain previously shown to be essential for regulation of hyphal growth, only at a paradoxical-growth concentration of caspofungin. Our results indicate that as opposed to micafungin, the increased [Ca
2+
]
c
at high concentrations of caspofungin activates calmodulin-calcineurin signaling at both a transcriptional and a posttranslational level and ultimately leads to paradoxical fungal growth.
Phase 1 Randomized, Double-Blind, Placebo-Controlled Study of RG7667, an Anticytomegalovirus Combination Monoclonal Antibody Therapy, in Healthy Adults
Authors: Ishida Julie H. , Burgess Tracy , Derby Michael A. , Brown Pearline A. , Maia Mauricio , Deng Rong , Emu Brinda , Feierbach Becket , Fouts Ashley E. , Liao X. Charlene , Tavel Jorge A.
Published: June 2015

Cytomegalovirus can cause debilitating and life-threatening disease in newborns infected
in utero
and immunocompromised individuals, including transplant recipients. RG7667 is a unique combination of two monoclonal antibodies that binds glycoprotein complexes on the surface of cytomegalovirus and inhibits its entry into host cells. A phase 1 first-in-human, randomized, double-blind, placebo-controlled, dose-escalation study of RG7667 given intravenously was conducted in 181 healthy adults. The study involved a single ascending dose stage (1, 3, 5, and 10 mg/kg each antibody;
n
= 21), a multiple ascending dose stage (5 and 10 mg/kg each antibody monthly for 3 doses;
n
= 10), and a multiple dose expansion stage (10 mg/kg each antibody monthly for 3 doses;
n
= 150). Subjects were followed for 85 to 141 days to evaluate safety, tolerability, pharmacokinetics, and immunogenicity. Most adverse events were mild, and the incidence of adverse events was similar among the RG7667 and placebo groups. RG7667 had dose-proportional pharmacokinetics in all three dosing stages, a mean terminal half-life of 20 to 30 days, and an overall pharmacokinetic profile consistent with that of a human monoclonal antibody that lacks endogenous host targets. The proportion of subjects developing an antitherapeutic antibody response was not higher in the RG7667 group than in the placebo group. In summary, single and multiple doses of RG7667 were found to be safe and well-tolerated in healthy adults and had a favorable pharmacokinetic and immunogenicity profile. This study supports further development of RG7667 as a therapy for the prevention and treatment of cytomegalovirus infection in susceptible populations. (This study has been registered at ClinicalTrials.gov under registration no. NCT01496755.)
Effect of Qnr on Plasmid Gyrase Toxins CcdB and ParE
Authors: Kwak Yee Gyung , Jacoby George A. , Hooper David C.
Published: June 2015

Plasmid toxins CcdB and ParE are part of addiction systems promoting plasmid maintenance. Both target host DNA gyrase, as do quinolones and plasmid-determined Qnr proteins that protect gyrase from quinolone inhibition. We cloned
qnrB4
,
qnrS1
,
ccdB
,
parE
, and the antitoxin-encoding genes
ccdA
and
parD
on compatible plasmids and tested them in combination. CcdB and ParE had no specific effect on quinolone susceptibility or Qnr protection, and Qnr did not act as a CcdB or ParE antitoxin.
Pharmacodynamic Profile of GSK2140944 against Methicillin-Resistant Staphylococcus aureus in a Murine Lung Infection Model
Authors: So Wonhee , Crandon Jared L. , Nicolau David P.
Published: June 2015

GSK2140944 is a novel bacterial type II topoisomerase inhibitor with
in vitro
activity against key causative respiratory pathogens, including methicillin-resistant
Staphylococcus aureus
(MRSA). We described the pharmacodynamics of GSK2140944 against MRSA in the neutropenic murine lung infection model. MICs of GSK2140944 were determined by broth microdilution. Plasma and epithelial lining fluid (ELF) pharmacokinetics were evaluated to allow determination of pulmonary distribution. Six MRSA isolates were tested. GSK2140944 doses of 1.56 to 400 mg/kg of body weight every 6 h (q6h) were utilized. Efficacy as the change in log
10
CFU at 24 h compared with 0 h controls and the area under the concentration-time curve for the free, unbound fraction of a drug (
f
AUC)/MIC required for various efficacy endpoints were determined. GSK2140944 MICs were 0.125 to 0.5 mg/liter against the six MRSA isolates. ELF penetration ratios ranged from 1.1 to 1.4. Observed maximal decreases were 1.1 to 3.1 log
10
CFU in neutropenic mice. The mean
f
AUC/MIC ratios required for stasis and 1-log-unit decreases were 59.3 ± 34.6 and 148.4 ± 83.3, respectively. GSK2140944 displayed
in vitro
and
in vivo
activity against MRSA. The pharmacodynamic profile of GSK2140944, as determined, supports its further development as a potential treatment option for pulmonary infections, including those caused by MRSA.
Mode of Action and Bactericidal Properties of Surotomycin against Growing and Nongrowing Clostridium difficile
Authors: Alam Mohammed Zahidul , Wu Xiaoqian , Mascio Carmela , Chesnel Laurent , Hurdle Julian G.
Published: June 2015

Surotomycin (CB-183,315), a cyclic lipopeptide, is in phase 3 clinical development for the treatment of
Clostridium difficile
infection. We report here the further characterization of the
in vitro
mode of action of surotomycin, including its activity against growing and nongrowing
C. difficile
. This was assessed through time-kill kinetics, allowing a determination of the effects on the membrane potential and permeability and macromolecular synthesis in
C. difficile
. Against representative strains of
C. difficile
, surotomycin displayed concentration-dependent killing of both logarithmic-phase and stationary-phase cultures at a concentration that was ≤16× the MIC. Exposure resulted in the inhibition of macromolecular synthesis (in DNA, RNA, proteins, and cell wall). At bactericidal concentrations, surotomycin dissipated the membrane potential of
C. difficile
without changes to the permeability of propidium iodide. These observations are consistent with surotomycin acting as a membrane-active antibiotic, exhibiting rapid bactericidal activities against growing and nongrowing
C. difficile
.
Persistent Staphylococcus aureus Isolates from Two Independent Cases of Bacteremia Display Increased Bacterial Fitness and Novel Immune Evasion Phenotypes
Authors: Richards R. L. , Haigh R. D. , Pascoe B. , Sheppard S. K. , Price F. , Jenkins D. , Rajakumar K. , Morrissey J. A.
Published: June 2015

Staphylococcus aureus
bacteremia cases are complicated by bacterial persistence and treatment failure despite the confirmed
in vitro
susceptibility of the infecting strain to administered antibiotics. A high incidence of methicillin-resistant
S. aureus
(MRSA) bacteremia cases are classified as persistent and are associated with poorer patient outcomes. It is still unclear how
S. aureus
evades the host immune system and resists antibiotic treatment for the prolonged duration of a persistent infection. In this study, the genetic changes and associated phenotypic traits specific to
S. aureus
persistent bacteremia were identified by comparing temporally dispersed isolates from persistent infections (persistent isolates) originating from two independent persistent
S. aureus
bacteremia cases with the initial infection isolates and with three resolved
S. aureus
bacteremia isolates from the same genetic background. Several novel traits were associated specifically with both independent sets of persistent
S. aureus
isolates compared to both the initial isolates and the isolates from resolved infections (resolved isolates). These traits included (i) increased growth under nutrient-poor conditions; (ii) increased tolerance of iron toxicity; (iii) higher expression of cell surface proteins involved in immune evasion and stress responses; and (iv) attenuated virulence in a
Galleria mellonella
larva infection model that was not associated with small-colony variation or metabolic dormancy such as had been seen previously. Whole-genome sequence analysis identified different single nucleotide mutations within the
mprF
genes of all the isolates with the adaptive persistence traits from both independent cases. Overall, our data indicate a novel role for MprF function during development of
S. aureus
persistence by increasing bacterial fitness and immune evasion.
A Plasmid-Borne System To Assess the Excision and Integration of Staphylococcal Cassette Chromosome
mec
Mediated by CcrA and CcrB
Authors: Wang Lei , Ahmed Mostafa H. , Safo Martin K. , Archer Gordon L.
Published: June 2015

Resistance to methicillin and other β-lactam antibiotics in staphylococci is due to
mecA
, which is carried on a genomic island, staphylococcal cassette chromosome
mec
(SCC
mec
). The chromosomal excision and integration of SCC
mec
are mediated by the site-specific recombinase CcrAB or CcrC, encoded within this element. A plasmid-borne system was constructed to assess the activities of CcrA and CcrB in the excision and integration of SCC
mec
in
Escherichia coli
and
Staphylococcus aureus
. The excision frequency in
E. coli
mediated by CcrAB from methicillin-resistant
S. aureus
(MRSA) strain N315 was only 9.2%, while the integration frequency was 31.4%. In
S. aureus
the excision and integration frequencies were 11.0% and 18.7%, respectively. Truncated mutants identified the N-terminal domain of either CcrB or CcrA to be necessary for both integration and excision, while the C-terminal domain was important for recombination efficiency. Site-directed mutagenesis of the N-terminal domain identified S11 and R79 of CcrA and S16, R89, T149, and R151 of CcrB to be residues essential for catalytic activities, and the critical location of these residues was consistent with a model of the tertiary structure of the N terminus of CcrA and CcrB. Furthermore, CcrAB and CcrC, cloned from a panel of 6 methicillin-resistant
S. aureus
strains and 2 methicillin-resistant
Staphylococcus epidermidis
strains carrying SCC
mec
types II, IV, and V, also catalyzed integration at rates 1.3 to 10 times higher than the rates at which they catalyzed excision, similar to the results from N315. The tendency of SCC
mec
integration to be favored over excision may explain the low spontaneous excision frequency seen among MRSA strains.

IMPORTANCE
Spontaneous excision of the genomic island (SCCmec) that encodes resistance to beta-lactam antibiotics (methicillin resistance) in staphylococci would convert a methicillin-resistant strain to a methicillin-susceptible strain, improving therapy of difficult-to-treat infections. This study characterizes a model system by which the relative frequencies of excision and integration can be compared. Using a plasmid-based model for excision and integration mediated by the recombinases CcrA and CcrB, integration occurred at a higher frequency than excision, consistent with the low baseline excision frequency seen in most strains. This model system can now be used to study conditions and drugs that may raise the SCC
mec
excision frequency and generate strains that are beta-lactam susceptible.
Structures of Capsular Polysaccharide Serotypes 35F and 35C of Streptococcus pneumoniae Determined by Nuclear Magnetic Resonance and Their Relation to Other Cross-Reactive Serotypes
Authors: Bush C. Allen , Cisar John O. , Yang Jinghua
Published: June 2015

The structures ofStreptococcus pneumoniaecapsular polysaccharides (CPSs) are essential for defining the antigenic as well as genetic relationships between CPS serotypes. The four serotypes that comprise CPS serogroup 35 (i.e., types 35F, 35A, 35B, and 35C) are known to cross-react with genetically related type 20, 29, 34, 42, or 47F. While the structures of CPS serotype 35A (CPS35A) and CPS35B are known, those of CPS35F and CPS35C are not. In the present study, the serotypes of CPS35F and CPS35C were characterized by high-resolution heteronuclear magnetic resonance (NMR) spectroscopy and glycosyl composition analyses to reveal the following repeat unit structures:where OAc indicates O-acetylated. Importantly, CPS35F, the immunizing serotype for the production of group 35 serum, more closely resembles CPS34 and CPS47F than other members of serogroup 35. Moreover, CPS35C is distinct from either CPS35F or CPS35B but closely related to CPS35A and identical to de-O-acetylated CPS42. The findings provide a comprehensive view of the structural and genetic relations that exist between the members of CPS serogroup 35 and other cross-reactive serotypes.

IMPORTANCECross-reactions of diagnostic rabbit antisera withStreptococcus pneumoniaecapsular polysaccharide serotypes are generally limited to members of the same serogroup. Exceptions do, however, occur, most notably among a group of nonvaccine serotypes that includes the members of serogroup 35 (i.e., types 35F, 35A, 35B, and 35C) and other genetically related types. The presently determined structures ofS. pneumoniaeserotypes 35F and 35C complete the structural characterization of serogroup 35 and thereby provide the first comprehensive description of how different members of this serogroup are related to each other and to types 29, 34, 42, and 47F. The structural and genetic features of these serotypes suggest the existence of three distinct capsular polysaccharide subgroups that presumably emerged by immune selection in the human host.
Characterization of an Unconventional Rhodopsin from the Freshwater Actinobacterium Rhodoluna lacicola
Authors: Keffer J. L. , Hahn M. W. , Maresca J. A.
Published: June 2015

Rhodopsin-encoding microorganisms are common in many environments. However, knowing that rhodopsin genes are present provides little insight into how the host cells utilize light. The genome of the freshwater actinobacterium
Rhodoluna lacicola
encodes a rhodopsin of the uncharacterized actinorhodopsin family. We hypothesized that actinorhodopsin was a light-activated proton pump and confirmed this by heterologously expressing
R. lacicola
actinorhodopsin in retinal-producing
Escherichia coli
. However, cultures of
R. lacicola
did not pump protons, even though actinorhodopsin mRNA and protein were both detected. Proton pumping in
R. lacicola
was induced by providing exogenous retinal, suggesting that the cells lacked the retinal cofactor. We used high-performance liquid chromatography (HPLC) and oxidation of accessory pigments to confirm that
R. lacicola
does not synthesize retinal. These results suggest that in some organisms, the actinorhodopsin gene is constitutively expressed, but rhodopsin-based light capture may require cofactors obtained from the environment.

IMPORTANCE
Up to 70% of microbial genomes in some environments are predicted to encode rhodopsins. Because most microbial rhodopsins are light-activated proton pumps, the prevalence of this gene suggests that in some environments, most microorganisms respond to or utilize light energy. Actinorhodopsins were discovered in an analysis of freshwater metagenomic data and subsequently identified in freshwater actinobacterial cultures. We hypothesized that actinorhodopsin from the freshwater actinobacterium
Rhodoluna lacicola
was a light-activated proton pump and confirmed this by expressing actinorhodopsin in retinal-producing
Escherichia coli
. Proton pumping in
R. lacicola
was induced only after both light and retinal were provided, suggesting that the cells lacked the retinal cofactor. These results indicate that photoheterotrophy in this organism and others may require cofactors obtained from the environment.
Clostridium difficile PCR Ribotype 018, a Successful Epidemic Genotype
Authors: Baldan Rossella , Trovato Alberto , Bianchini Valentina , Biancardi Anna , Cichero Paola , Mazzotti Maria , Nizzero Paola , Moro Matteo , Ossi Cristina , Scarpellini Paolo , Cirillo Daniela Maria
Published: June 2015

Clostridium difficile
infection (CDI) became a public health problem for the global spreading of the so-called hypervirulent PCR ribotypes (RTs) 027 and 078, associated with increases in the transmission and severity of the disease. However, especially in Europe, several RTs are prevalent, and the concept of hypervirulence is currently debated. We investigated the toxin and resistance profiles and the genetic relatedness of 312
C. difficile
strains isolated in a large Italian teaching hospital during a 5-year period. We evaluated the role of CDI-related antibiotic consumption and infection control practices on the RT predominance in association with their molecular features and transmission capacity. Excluding secondary cases due to nosocomial transmission, RT018 was the predominant genotype (42.4%) followed by RT078 (13.6%), while RT027 accounted for 0.8% of the strains. RT078 was most frequently isolated from patients in intensive care units. Its prevalence significantly increased over time, but its transmission capacity was very low. In contrast, RT018 was highly transmissible and accounted for 95.7% of the secondary cases. Patients with the RT018 genotype were significantly older than those with RT078 and other RTs, indicating an association between epidemic RT and age. We provide here the first epidemiological evidence to consider RT018 as a successful epidemic genotype that deserves more attention in clinical practice.
Examination of the Enterotoxigenic Escherichia coli Population Structure during Human Infection
Authors: Sahl Jason W. , Sistrunk Jeticia R. , Fraser Claire M. , Hine Erin , Baby Nabilah , Begum Yasmin , Luo Qingwei , Sheikh Alaullah , Qadri Firdausi , Fleckenstein James M. , Rasko David A.
Published: June 2015

Enterotoxigenic
E. coli
(ETEC) can cause severe diarrhea and death in children in developing countries; however, bacterial diversity in natural infection is uncharacterized. In this study, we explored the natural population variation of ETEC from individuals with cholera-like diarrhea. Genomic sequencing and comparative analysis of multiple ETEC isolates from twelve cases of severe diarrhea demonstrated clonal populations in the majority of subjects (10/12). In contrast, a minority of individuals (2/12) yielded phylogenomically divergent ETEC isolates. Detailed examination revealed that isolates also differed in virulence factor content. These genomic data suggest that severe, cholera-like ETEC infections are largely caused by a clonal population of organisms within individual patients. Additionally, the isolation of similar clones from geographically and temporally dispersed cases with similar clinical presentations suggests that some isolates are particularly suited for virulence. The identification of multiple genomically diverse isolates with variable virulence factor profiles from a single subject highlights the dynamic nature of ETEC, as well as a potential weakness in the examination of cultures obtained from a single colony in clinical settings. These findings have implications for vaccine design and provide a framework for the study of population variation in other human pathogens.

IMPORTANCE
Enterotoxigenic
Escherichia coli
(ETEC) has been identified as one of the major causes of diarrheal diseases in children as well as travelers. It has been previously appreciated that this pathogenic variant of
E. coli
is diverse, both at the genomic level, as defined with multilocus sequence typing, and with regard to the presence or absence of virulence factors within clonal groups. Using whole-genome sequencing and comparative analysis, we identified and characterized diverse enterotoxigenic
E. coli
isolates from individual patients. In 17% of patients, we identified multiple distinct ETEC isolates, each with unique genomic features and in some cases diverse virulence factor profiles. These studies ascertained that any one person may be colonized by multiple pathogenic ETEC isolates, which may impact how we think about the development of vaccines and therapeutics against these organisms.
The Atypical Occurrence of Two Biotin Protein Ligases in Francisella novicida Is Due to Distinct Roles in Virulence and Biotin Metabolism
Authors: Feng Youjun , Chin Chui-Yoke , Chakravartty Vandana , Gao Rongsui , Crispell Emily K. , Weiss David S. , Cronan John E.
Published: June 2015

The physiological function of biotin requires biotin protein ligase activity in order to attach the coenzyme to its cognate proteins, which are enzymes involved in central metabolism. The model intracellular pathogen
Francisella novicida
is unusual in that it encodes two putative biotin protein ligases rather than the usual single enzyme.
F. novicida
BirA has a ligase domain as well as an N-terminal DNA-binding regulatory domain, similar to the prototypical BirA protein in
E. coli
. However, the second ligase, which we name BplA, lacks the N-terminal DNA binding motif. It has been unclear why a bacterium would encode these two disparate biotin protein ligases, since
F. novicida
contains only a single biotinylated protein.
In vivo
complementation and enzyme assays demonstrated that BirA and BplA are both functional biotin protein ligases, but BplA is a much more efficient enzyme. BirA, but not BplA, regulated transcription of the biotin synthetic operon. Expression of
bplA
(but not
birA
) increased significantly during
F. novicida
infection of macrophages. BplA (but not BirA) was required for bacterial replication within macrophages as well as in mice. These data demonstrate that
F. novicida
has evolved two distinct enzymes with specific roles; BplA possesses the major ligase activity, whereas BirA acts to regulate and thereby likely prevent wasteful synthesis of biotin. During infection BplA seems primarily employed to maximize the efficiency of biotin utilization without limiting the expression of biotin biosynthetic genes, representing a novel adaptation strategy that may also be used by other intracellular pathogens.

IMPORTANCE
Our findings show that
Francisella novicida
has evolved two functional biotin protein ligases, BplA and BirA. BplA is a much more efficient enzyme than BirA, and its expression is significantly induced upon infection of macrophages. Only BplA is required for
F. novicida
pathogenicity, whereas BirA prevents wasteful biotin synthesis. These data demonstrate that the atypical occurrence of two biotin protein ligases in
F. novicida
is linked to distinct roles in virulence and biotin metabolism.
Brachial artery pseudoaneurysm arising from the stump of a ligated arteriovenous fistula
Authors: Cox Nicola , Sahnan Kapil , Yee Chris Pui Yan , Sritharan Kaji
Published: June 2015

An 85-year-old man presented to A&E department with a bleeding, pulsatile mass within the left antecubital fossa. He reported a 3-month history of an increasing, painless swelling. He had a history of end-stage renal failure secondary to antiglomerular basement membrane disease. 14 years prior, he had a left brachiocephalic fistula created, which was ligated shortly after its creation due to Steal syndrome. Examination revealed a 10×15×10 cm pulsatile, non-tender mass with overlying ulceration in the left antecubital fossa. Arterial duplex demonstrated a pseudoaneurysm arising from the left distal brachial artery with a 9 mm neck. The patient underwent surgical exploration and repair. At surgery, a large brachial artery pseudoaneurysm at the site of the previous fistula ligation was found. The overlying ulcerated skin and pseudoaneurysm were excised en mass, and the arterial defect repaired by transection and end-to-end anastomosis. This is the first reported case of a brachial artery pseudoaneurysm occurring following arteriovenous fistula ligation.
Immune reconstitution inflammatory syndrome in a patient with progressive multifocal leukoencephalopathy
Authors: Shahani Lokesh , Shah Minal , Tavakoli-Tabasi Shahriar
Published: June 2015

Progressive multifocal leukoencephalopathy (PML) is a severe opportunistic infection of the central nervous system. A 52-year-old man with HIV infection, recently started on antiretroviral therapy, presented with symptoms of mental cloudiness, blurry vision and ataxia. MRI of the brain showed nodular perivascular space enhancement with surrounding vasogenic oedema and midline shift. A lumbar puncture revealed non-inflammatory cerebrospinal fluid and was positive for JC virus. As the patient developed worsening symptoms in the setting of initiation of antiretroviral therapy with immune recovery, a diagnosis of JC virus-associated immune reconstitution inflammatory syndrome (IRIS) was made. With recent literature on the use of CCR5 antagonist maraviroc in PML, our patient was started on maraviroc and noted to have improvement in PML IRIS. This is the first case of an HIV-positive patient successfully treated for PML IRIS with maraviroc, as verified by our literature review; also, our case has clinical implications in improving outcome in PML IRIS.
Peripheral ameloblastoma of gingiva with cytokeratin 19 analysis
Authors: Chhina Shivjot , Rathore Ajit Singh
Published: June 2015

A 42-year-old woman presented with a gingival mass in the lingual vestibule of the mandibular incisor premolar region. On intraoral examination, the swelling was non-tender and firm. Surgical excision was carried out and subsequent histopathological examination revealed areas resembling ameloblastoma-like and basaloid areas with atypical features suggestive of basal cell carcinoma. Immunohistochemical analysis was carried out to ascertain the origin of the lesion.
Scoping review of physical rehabilitation interventions in long-term care: protocol for tools, models of delivery, outcomes and quality indicators
Authors: McArthur Caitlin , Gibbs Jenna , Papaioannou Alexandra , Hirdes John , Milligan James , Berg Katherine , Giangregorio Lora
Published: June 2015

Introduction

A growing number of medically complex older adults reside in long-term care (LTC) and often require physical rehabilitation (PR). While PR is effective at maintaining or improving a patient's physical function, the breadth of PR interventions evaluated in LTC, which outcomes or quality indicators (QI) can be used to evaluate PR, and what tools or models can be used to determine eligibility for PR services remain unknown.

Methods and analysis

A scoping review will be conducted to address the following research questions: (1) What types of PR have been evaluated for efficacy or effectiveness in LTC? (2) Which outcomes or QIs have been used when evaluating PR interventions in LTC, and how can this inform evaluation of PR using existing QIs in the Canadian context? (3) What tools or models exist or have been validated for decision-making in the allocation of PR resources in LTC? We will conduct a comprehensive literature search in MEDLINE, EMBASE, CINAHL, Cochrane Database of Systematic Reviews, Physiotherapy Evidence Database (PEDro) and Occupational Therapy Systematic Evaluation of Evidence database (OTseeker) and a structured grey literature search. Two team members will screen articles and abstract the data. The results will be displayed according to the research question they address. Data abstracted regarding outcomes and QIs will be mapped onto existing, publicly reported QIs used in Ontario, Canada.

Ethics and dissemination

The scoping review will synthesise the characteristics of PR interventions described in the literature, the outcomes used to evaluate them and tools to determine eligibility for services. The review will be the first step in formally identifying what outcomes and QIs have been used to evaluate PR in LTC, and will be used to inform a stakeholder consensus process exploring the same question. The scoping review may also identify knowledge gaps. The results will be disseminated via publication and presentation at conferences, in addition to a 1-day stakeholder meeting.