bluuebunny/crossref_metadata_2025_split huggingface dataset:
Stromatoporoid growth forms and Devonian reef fabrics in the Upper Devonian Alexandra Reef System, Canada – Insight on the challenges of applying Devonian reef facies models
Authors: MacNeil Alex J. , Jones Brian 
Published: February 2016

AbstractExisting facies models for Devonian reef systems can be divided into high‐energy and low‐energy types. A number of assumptions have been made in the development of these models and, in some cases, criteria that distinguish important aspects of the models are poorly defined. The Upper Devonian Alexandra Reef System contains a variety of reef fabrics from different depositional environments and is ideal for studying the range of environments in which stromatoporoids thrived and the facies from these different environments. A wide variety of stromatoporoid growth forms including laminar, tabular, anastamosing laminar and tabular, domal, bulbous, dendroid, expanding conical, concave‐up whorled‐laminar, concave‐up massive tabular and platy‐multicolumnar are present in the Alexandra Reef System. The whorled‐laminar and massive tabular concave‐up growth forms are virtually undocumented from other Devonian reefs but were common in the reef front of the Alexandra, where they thrived in a low‐energy environment around and below fair‐weather wave base. In contrast, high‐energy parts of the reef margin were dominated by bioclastic rubble deposits with narrow ribbon‐like discontinuous bodies of laminar stromatoporoid framestone. In the lagoon, laminar stromatoporoids formed steep‐sided sediment‐dominated bioherms in response to sea‐level rise and flooding. Relying mostly on the different reef facies in the Alexandra system, a new classification scheme for Devonian reef fabrics has been developed. Devonian reef fabrics can be classified as being: (i) sediment‐laden metazoan dominated; (ii) metazoan–microbial dominated (boundstone); (iii) metazoan dominated (framestone); or (iv) metazoan–marine cement dominated. Distinction of these fabrics carries important sedimentary and palaeoecological implications for reconstructing the depositional environment. With examples from the Alexandra Formation, it is demonstrated that reef facies accumulated in a range of depositional environments and that the simple observation of massive stromatoporoids with or without microbial deposits does not automatically imply a high‐energy reef margin, as otherwise portrayed in a number of the existing facies models for these systems.
Effects of Nordic walking training on functional parameters in Parkinson's disease: a randomized controlled clinical trial
Authors: Monteiro E.P. , Franzoni L.T. , Cubillos D.M. , de Oliveira Fagundes A. , Carvalho A.R. , Oliveira H.B. , Pantoja P.D. , Schuch F.B. , Rieder C.R. , Martinez F.G. , Peyré‐Tartaruga L.A. 
Published: February 2016

We compare the effects of Nordic walking training (NW) and Free walk (FW) on functional parameters (motor symptoms, balance) and functional mobility (Timed Up and Go at Self‐selected Speed – TUGSS, and at forced speed, TUGFS; Self‐selected Walking Speed, SSW; locomotor rehabilitation index, LRI) of Parkinson's disease (PD) patients. The study included 33 patients with clinical diagnosis of idiopathic PD, and staging between 1 and 4 in the Hoehn and Yahr scale (H&Y) randomized into two groups: NW (N = 16) and FW (N = 17) for 6 weeks. Baseline characteristics were compared trough a one‐way ANOVA. Outcomes were analyzed using the Generalized Estimation Equations (GEE) with a Bonferroni post‐hoc. Data were analyzed using SPSS v.20.0. Improvements in UPDRS III (P < 0.001), balance scores (P < 0.035), TUGSS distance (P < 0.001), TUGFS distance (P < 0.001), SSW (P < 0.001), and LRI (P < 0.001) were found for both groups. However, the NW group showed significant differences (P < 0.001) when compared to the FW group for the functional mobility. We conclude the NW improves functional parameters and walking mobility demonstrating that NW is as effective as the FW, including benefits for FW on the functional mobility of people with PD.
Teaching the assessment of normality using large easily‐generated real data sets
Authors: Kulp Christopher W. , Sprechini Gene D. 
Published: February 2016

SummaryA classroom activity is presented, which can be used in teaching students statistics with an easily generated, large, real world data set. The activity consists of analyzing a video recording of an object. The colour data of the recorded object can then be used as a data set to explore variation in the data using graphs including histograms, quantile–quantile plots and scatterplots, and to indicate possible formal analyses.
SPAWNN: A Toolkit for SPatial Analysis With Self‐Organizing Neural Networks
Authors: Hagenauer Julian , Helbich Marco 
Published: February 2016

AbstractThis article introduces the SPAWNN toolkit, an innovative toolkit for spatial analysis with self‐organizing neural networks, which is published as free and open‐source software (http://www.spawnn.org). It extends existing toolkits in three important ways. First, the SPAWNN toolkit distinguishes between self‐organizing neural networks and spatial context models with which the networks can be combined to incorporate spatial dependence and provides implementations for both. This distinction maintains modularity and enables a multitude of useful combinations for analyzing spatial data with self‐organizing neural networks. Second, SPAWNN interactively links different self‐organizing networks and data visualizations in an intuitive manner to facilitate explorative data analysis. Third, it implements cutting‐edge clustering algorithms for identifying clusters in the trained networks. Toolkits such as SPAWNN are particularly needed when researchers and practitioners are confronted with large amounts of complex and high‐dimensional data. The computational performance of the implemented algorithms is empirically demonstrated using high‐dimensional synthetic data sets, while the practical functionality highlighting the distinctive features of the toolkit is illustrated with a case study using socioeconomic data of the city of Philadelphia, Pennsylvania.
The modified corneocyte surface area measurement as an index of epidermal barrier properties: inverse correlation with transepidermal water loss
Authors: Momota Yutaka , Shimada Kenichiro , Noguchi Azusa , Saito Akio , Nozawa Satoshi , Niina Ayaka , Tani Kenji , Azakami Daigo , Ishioka Katsumi , Sako Toshinori 
Published: February 2016

BackgroundCorneocyte surface area (CSA) is as established parameter for skin barrier function in humans. Measurement of canine CSA has been previously reported but has not been validated.Hypothesis/ObjectivesThe aim of this study was to evaluate the validity of CSA as a barrier function parameter in dogs.AnimalsSix clinically normal beagle dogs.MethodsCSA was measured and compared with transepidermal water loss (TEWL) using sequential tape stripping of the stratum corneum as a model of acute barrier disruption. Then, CSA and TEWL were measured at four anatomical sites (groin, lower back, nasal bridge and pinna). The correlation between the two indices was also evaluated.ResultsFrom the results of sequential tape stripping, CSA values gradually decreased with increasing number of tape strippings. The CSA values were inversely correlated with the TEWL ones. The two indices at different sites were variable and were strongly correlated.Conclusions and clinical importanceCanine CSA was demonstrated to be a useful parameter for the canine skin barrier function. The results from the anatomical sites imply that the cephalic sites (nasal bridge and pinna) were lower than others in skin barrier function.
Perpetuation of torsade de pointes in heterogeneous hearts: competing foci or re‐entry?
Authors: Vandersickel Nele , de Boer Teun P. , Vos Marc A. , Panfilov Alexander V. 
Published: February 2016

Key points
The underlying mechanism of torsade de pointes (TdP) remains of debate: perpetuation may be due to (1) focal activity or (2) re‐entrant activity.
The onset of TdP correlates with action potential heterogeneities in different regions of the heart.
We studied the mechanism of perpetuation of TdP in silico using a 2D model of human cardiac tissue and an anatomically accurate model of the ventricles of the human heart.
We found that the mechanism of perpetuation TdP depends on the degree of heterogeneity. If the degree of heterogeneity is large, focal activity alone can sustain a TdP, otherwise re‐entrant activity emerges.
This result can help to understand the relationship between the mechanisms of TdP and tissue properties and may help in developing new drugs against it.
AbstractTorsade de pointes (TdP) can be the consequence of cardiac remodelling, drug effects or a combination of both. The mechanism underlying TdP is unclear, and may involve triggered focal activity or re‐entry. Recent work by our group has indicated that both cases may exist, i.e. TdPs induced in the chronic atrioventricular block (CAVB) dog model may have a focal origin or are due to re‐entry. Also it was found that heterogeneities might play an important role. In the current study we have used computational modelling to further investigate the mechanisms involved in TdP initiation and perpetuation, especially in the CAVB dog model, by the addition of heterogeneities with reduced repolarization reserve in comparison with the surrounding tissue. For this, the TNNP computer model was used for computations. We demonstrated in 2D and 3D simulations that ECGs with the typical TdP morphology can be caused by both multiple competing foci and re‐entry circuits as a result of introduction of heterogeneities, depending on whether the heterogeneities have a large or a smaller reduced repolarization reserve in comparison with the surrounding tissue. Large heterogeneities can produce ectopic TdP, while smaller heterogeneities will produce re‐entry‐type TdP.
Cherenkov imaging method for rapid optimization of clinical treatment geometry in total skin electron beam therapy
Authors: Andreozzi Jacqueline M. , Zhang Rongxiao , Gladstone David J. , Williams Benjamin B. , Glaser Adam K. , Pogue Brian W. , Jarvis Lesley A. 
Published: February 2016

Purpose:A method was developed utilizing Cherenkov imaging for rapid and thorough determination of the two gantry angles that produce the most uniform treatment plane during dual‐field total skin electron beam therapy (TSET).Methods:Cherenkov imaging was implemented to gather 2D measurements of relative surface dose from 6 MeV electron beams on a white polyethylene sheet. An intensified charge‐coupled device camera time‐gated to the Linac was used for Cherenkov emission imaging at sixty‐two different gantry angles (1° increments, from 239.5° to 300.5°). Following a modified Stanford TSET technique, which uses two fields per patient position for full body coverage, composite images were created as the sum of two beam images on the sheet; each angle pair was evaluated for minimum variation across the patient region of interest. Cherenkov versus dose correlation was verified with ionization chamber measurements. The process was repeated at source to surface distance (SSD) = 441, 370.5, and 300 cm to determine optimal angle spread for varying room geometries. In addition, three patients receiving TSET using a modified Stanford six‐dual field technique with 6 MeV electron beams at SSD = 441 cm were imaged during treatment.Results:As in previous studies, Cherenkov intensity was shown to directly correlate with dose for homogenous flat phantoms (R2 = 0.93), making Cherenkov imaging an appropriate candidate to assess and optimize TSET setup geometry. This method provided dense 2D images allowing 1891 possible treatment geometries to be comprehensively analyzed from one data set of 62 single images. Gantry angles historically used for TSET at their institution were 255.5° and 284.5° at SSD = 441 cm; however, the angles optimized for maximum homogeneity were found to be 252.5° and 287.5° (+6° increase in angle spread). Ionization chamber measurements confirmed improvement in dose homogeneity across the treatment field from a range of 24.4% at the initial angles, to only 9.8% with the angles optimized. A linear relationship between angle spread and SSD was observed, ranging from 35° at 441 cm, to 39° at 300 cm, with no significant variation in percent‐depth dose at midline (R2 = 0.998). For patient studies, factors influencing in vivo correlation between Cherenkov intensity and measured surface dose are still being investigated.Conclusions:Cherenkov intensity correlates to relative dose measured at depth of maximum dose in a uniform, flat phantom. Imaging of phantoms can thus be used to analyze and optimize TSET treatment geometry more extensively and rapidly than thermoluminescent dosimeters or ionization chambers. This work suggests that there could be an expanded role for Cherenkov imaging as a tool to efficiently improve treatment protocols and as a potential verification tool for routine monitoring of unique patient treatments.
Bidirectional Transfer of Raltegravir in an
Ex Vivo
Human Cotyledon Perfusion Model
Authors: Vinot Cécile , Tréluyer Jean-Marc , Giraud Carole , Gavard Laurent , Peytavin Gilles , Mandelbrot Laurent 
Published: February 2016

ABSTRACT

Placental transfer of the HIV integrase inhibitor raltegravir (RLT) was investigated in term human cotyledons in the maternal-to-fetal (
n
= 3) and fetal-to-maternal (
n
= 6) directions. In the maternal-to-fetal direction, the mean ± standard deviation (SD) fetal transfer rate (FTR) was 9.1% ± 1.4%, and the mean ± SD clearance index (IC), i.e., RLT FTR/antipyrine FTR, was 0.28 ± 0.05. In the fetal-to-maternal direction, the mean ± SD CI was 0.31 ± 0.09. Placental transfer of RLT was high in both directions.
OligoG CF-5/20 Disruption of Mucoid Pseudomonas aeruginosa Biofilm in a Murine Lung Infection Model
Authors: Hengzhuang Wang , Song Zhijun , Ciofu Oana , Onsøyen Edvar , Rye Philip D. , Høiby Niels 
Published: February 2016

ABSTRACT

Biofilm growth is a universal survival strategy for bacteria, providing an effective and resilient approach for survival in an otherwise hostile environment. In the context of an infection, a biofilm provides resistance and tolerance to host immune defenses and antibiotics, allowing the biofilm population to survive and thrive under conditions that would destroy their planktonic counterparts. Therefore, the disruption of the biofilm is a key step in eradicating persistent bacterial infections, as seen in many types of chronic disease. In these studies, we used both
in vitro
minimum biofilm eradication concentration (MBEC) assays and an
in vivo
model of chronic biofilm infection to demonstrate the biofilm-disrupting effects of an alginate oligomer, OligoG CF-5/20. Biofilm infections were established in mice by tracheal instillation of a mucoid clinical isolate of
Pseudomonas aeruginosa
embedded in alginate polymer beads. The disruption of the biofilm by OligoG CF-5/20 was observed in a dose-dependent manner over 24 h, with up to a 2.5-log reduction in CFU in the infected mouse lungs. Furthermore,
in vitro
assays showed that 5% OligoG CF-5/20 significantly reduced the MBEC for colistin from 512 μg/ml to 4 μg/ml after 8 h. These findings support the potential for OligoG CF-5/20 as a biofilm disruption agent which may have clinical value in reducing the microbial burden in chronic biofilm infections.
A High-Affinity Native Human Antibody Disrupts Biofilm from Staphylococcus aureus Bacteria and Potentiates Antibiotic Efficacy in a Mouse Implant Infection Model
Authors: Estellés Angeles , Woischnig Anne-Kathrin , Liu Keyi , Stephenson Robert , Lomongsod Evelene , Nguyen Da , Zhang Jianzhong , Heidecker Manfred , Yang Yifan , Simon Reyna J. , Tenorio Edgar , Ellsworth Stote , Leighton Anton , Ryser Stefan , Gremmelmaier Nina Khanna , Kauvar Lawrence M. 
Published: February 2016

ABSTRACT

Many serious bacterial infections are difficult to treat due to biofilm formation, which provides physical protection and induces a sessile phenotype refractory to antibiotic treatment compared to the planktonic state. A key structural component of biofilm is extracellular DNA, which is held in place by secreted bacterial proteins from the DNABII family: integration host factor (IHF) and histone-like (HU) proteins. A native human monoclonal antibody, TRL1068, has been discovered using single B-lymphocyte screening technology. It has low-picomolar affinity against DNABII homologs from important Gram-positive and Gram-negative bacterial pathogens. The disruption of established biofilm was observed
in vitro
at an antibody concentration of 1.2 μg/ml over 12 h. The effect of TRL1068
in vivo
was evaluated in a murine tissue cage infection model in which a biofilm is formed by infection with methicillin-resistant
Staphylococcus aureus
(MRSA; ATCC 43300). Treatment of the established biofilm by combination therapy of TRL1068 (15 mg/kg of body weight, intraperitoneal [i.p.] administration) with daptomycin (50 mg/kg, i.p.) significantly reduced adherent bacterial count compared to that after daptomycin treatment alone, accompanied by significant reduction in planktonic bacterial numbers. The quantification of TRL1068 in sample matrices showed substantial penetration of TRL1068 from serum into the cage interior. TRL1068 is a clinical candidate for combination treatment with standard-of-care antibiotics to overcome the drug-refractory state associated with biofilm formation, with potential utility for a broad spectrum of difficult-to-treat bacterial infections.
Prediction of Fluoroquinolone Resistance in Gram-Negative Bacteria Causing Bloodstream Infections
Authors: Dan Seejil , Shah Ansal , Justo Julie Ann , Bookstaver P. Brandon , Kohn Joseph , Albrecht Helmut , Al-Hasan Majdi N. 
Published: February 2016

ABSTRACT
Increasing rates of fluoroquinolone resistance (FQ-R) have limited empirical treatment options for Gram-negative infections, particularly in patients with severe beta-lactam allergy. This case-control study aims to develop a clinical risk score to predict the probability of FQ-R in Gram-negative bloodstream isolates. Adult patients with Gram-negative bloodstream infections (BSI) hospitalized at Palmetto Health System in Columbia, South Carolina, from 2010 to 2013 were identified. Multivariate logistic regression was used to identify independent risk factors for FQ-R. Point allocation in the fluoroquinolone resistance score (FQRS) was based on regression coefficients. Model discrimination was assessed by the area under receiver operating characteristic curve (AUC). Among 824 patients with Gram-negative BSI, 143 (17%) had BSI due to fluoroquinolone-nonsusceptible Gram-negative bacilli. Independent risk factors for FQ-R and point allocation in FQRS included male sex (adjusted odds ratio [aOR], 1.97; 95% confidence intervals [CI], 1.36 to 2.98; 1 point), diabetes mellitus (aOR, 1.54; 95% CI, 1.03 to 2.28; 1 point), residence at a skilled nursing facility (aOR, 2.28; 95% CI, 1.42 to 3.63; 2 points), outpatient procedure within 30 days (aOR, 3.68; 95% CI, 1.96 to 6.78; 3 points), prior fluoroquinolone use within 90 days (aOR, 7.87; 95% CI, 4.53 to 13.74; 5 points), or prior fluoroquinolone use within 91 to 180 days of BSI (aOR, 2.77; 95% CI, 1.17 to 6.16; 3 points). The AUC for both final logistic regression and FQRS models was 0.73. Patients with an FQRS of 0, 3, 5, or 8 had predicted probabilities of FQ-R of 6%, 22%, 39%, or 69%, respectively. The estimation of patient-specific risk of antimicrobial resistance using FQRS may improve empirical antimicrobial therapy and fluoroquinolone utilization in Gram-negative BSI.
Whole-Genome Sequence of a
bla
OXA-48
-Harboring Raoultella ornithinolytica Clinical Isolate from Lebanon
Authors: Al-Bayssari Charbel , Olaitan Abiola Olumuyiwa , Leangapichart Thongpan , Okdah Liliane , Dabboussi Fouad , Hamze Monzer , Rolain Jean-Marc 
Published: February 2016

ABSTRACT

We analyzed the whole-genome sequence of a
bla
OXA-48
-harboring
Raoultella ornithinolytica
clinical isolate from a patient in Lebanon. The size of the
Raoultella ornithinolytica
CMUL058 genome was 5,622,862 bp, with a G+C content of 55.7%. We deciphered all the molecular mechanisms of antibiotic resistance, and we compared our genome to other available
R. ornithinolytica
genomes in GenBank. The resistome consisted of 9 antibiotic resistance genes, including a plasmidic
bla
OXA-48
gene whose genetic organization is also described.
Linezolid Surveillance Results for the United States (LEADER Surveillance Program 2014)
Authors: Flamm Robert K. , Mendes Rodrigo E. , Hogan Patricia A. , Streit Jennifer M. , Ross James E. , Jones Ronald N. 
Published: February 2016

ABSTRACT

The
l
inezolid
e
xperience and
a
ccurate
d
etermination of
r
esistance (LEADER) surveillance program has monitored linezolid activity, spectrum, and resistance since 2004. In 2014, a total of 6,865 Gram-positive pathogens from 60 medical centers from 36 states were submitted. The organism groups evaluated were
Staphylococcus aureus
(3,106), coagulase-negative staphylococci (CoNS; 797), enterococci (855),
Streptococcus pneumoniae
(874), viridans group streptococci (359), and beta-hemolytic streptococci (874). Susceptibility testing was performed by reference broth microdilution at the monitoring laboratory. Linezolid-resistant isolates were confirmed by repeat testing. PCR and sequencing were performed to detect mutations in 23S rRNA, L3, L4, and L22 proteins and acquired genes (
cfr
and
optrA
). The MIC
50/90
for
Staphylococcus aureus
was 1/1 μg/ml, with 47.2% of isolates being methicillin-resistant
Staphylococcus aureus
. Linezolid was active against all
Streptococcus pneumoniae
strains and beta-hemolytic streptococci with a MIC
50/90
of 1/1 μg/ml and against viridans group streptococci with a MIC
50/90
of 0.5/1 μg/ml. Among the linezolid-nonsusceptible MRSA strains, one strain harbored
cfr
only (MIC, 4 μg/ml), one harbored G2576T (MIC, 8 μg/ml), and one contained
cfr
and G2576T with L3 changes (MIC, ≥8 μg/ml). Among CoNS, 0.75% (six isolates) of all strains demonstrated linezolid MIC results of ≥4 μg/ml. Five of these were identified as
Staphylococcus epidermidis
, four of which contained
cfr
in addition to the presence of mutations in the ribosomal proteins L3 and L4, alone or in combination with 23S rRNA (G2576T) mutations. Six enterococci (0.7%) were linezolid nonsusceptible (≥4 μg/ml; five with G2576T mutations, including one with an additional
cfr
gene, and one strain with
optrA
only). Linezolid demonstrated excellent activity and a sustained susceptibility rate of 99.78% overall.