bluuebunny/crossref_metadata_2025_split huggingface dataset:
Architecture of the superintegron in Vibrio cholerae: identification of core and unique genes
Authors: Marin Michel A , Vicente Ana Carolina P 
Published: May 2013

Background: Vibrio cholerae, the etiologic agent of cholera, is indigenous to aquatic environments. The V. cholerae genome consists of two chromosomes; the smallest of these harbors a large gene capture and excision system called the superintegron (SI), of ~120 kbp. The flexible nature of the SI that results from gene cassette capture, deletion and rearrangement is thought to make it a hotspot of V. cholerae diversity, but beyond the basic structure it is not clear if there is a core genome in the SI and if so how it is structured. The aim of this study was to explore the core genome structure and the differences in gene content among strains of V. cholerae.Methods: From the complete genomes of seven V. cholerae and one Vibrio mimicus representative strains, we recovered the SI sequences based on the locations of the structural gene IntI4 and the V. cholerae repeats. Analysis of the pangenome, including cluster analysis of functional genes, pangenome profile analysis, genetic variation analysis of functional genes, strain evolution analysis and function enrichment analysis of gene clusters, was performed using a pangenome analysis pipeline in addition to the R scripts, splitsTree4 and genoPlotR.Results and conclusions: Here, we reveal the genetic architecture of the V. cholerae SI. It contains eight core genes when V. mimicus is included and 21 core genes when only V. cholerae strains are considered; many of them are present in several copies. The V. cholerae SI has an open pangenome, which means that V. cholerae may be able to import new gene cassettes to SI. The set of dispensable SI genes is influenced by the niche and type species. The core genes are distributed along the SI, apparently without a position effect.
The Impact of Pharmacist-Directed Patient Education and Anticoagulant Care Coordination on Patient Satisfaction
Authors: Makowski Charles T , Jennings Douglas L , Nemerovski Carrie W , Szandzik Edward G , Kalus James S 
Published: May 2013

BACKGROUND: Patient satisfaction data played a role in determining Medicare reimbursement as of October 2012. Clinical pharmacy services could improve satisfaction of hospital inpatients but it is unclear whether this relates to performance on standardized hospital surveys. OBJECTIVE: To describe the impact on patient satisfaction of patient education and follow-up care coordination provided by an inpatient pharmacist-directed anticoagulation service (PDAS). METHODS: This study was conducted at an urban, tertiary care hospital. PDAS is a clinical pharmacy service that has improved transition-of-care, safety, and efficacy involving anticoagulation at our institution. Patients receiving inpatient anticoagulation during February 2001-April 2007 (pre-PDAS) and December 2008-December 2010 (post-PDAS), who responded to a mail-in survey, were included. Survey items included satisfaction (“How satisfied were you with the medical care?”), amount of information (“Was the amount of information you received about your medicine…?”), clarity of information (“Was the clarity of the information about your medicine…?”), answer quality (“Were the answers to your questions about your medicine…?”), and spoke to a pharmacist (“Did a pharmacist speak with you during your stay?”). Response options for amount of information, clarity of information, answer quality, and satisfaction used a symmetric 5-point Likert-type scale, with options 1-5 indicating most to least positive, respectively. Options 1-2 were considered positive and options 3-5 were considered negative. Primary analysis compared patient satisfaction (defined as rate of positive responses) between pre-PDAS and post-PDAS respondents. χ2 Test was used for all comparisons. RESULTS: Surveys were distributed to 1694 patients after discharge, with 687 (40.6%) responding. Post-PDAS respondents had improved patient satisfaction for all positive response items, compared to pre-PDAS scores. Amount of information increased by 37.2%, clarity of information increased by 35.2%, answer quality increased by 29.5%, and satisfaction increased by 10.6% (p < 0.001 for all comparisons). CONCLUSIONS: Hospitals deploying focused programs with systematic approaches to patient-pharmacist communication may positively impact patient satisfaction.
Companion Biomarkers: Paving the Pathway to Personalized Treatment for Cancer
Authors: Duffy Michael J , Crown John 
Published: May 2013

BACKGROUND
Companion biomarkers are biomarkers that are used in combination with specific therapies and that prospectively help predict likely response or severe toxicity. In this article we review the role of companion biomarkers in guiding treatment in patients with cancer.

CONTENT
In addition to the established companion biomarkers such as estrogen receptors and HER2 (human epidermal growth factor receptor 2) in breast cancer, several new companion biomarkers have become available in recent years. These include v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS) mutations for the selection of patients with advanced colorectal cancer who are unlikely to benefit from anti–epidermal growth factor receptor antibodies (cetuximab or panitumumab), epidermal growth factor receptor (EGFR) mutations for selecting patients with advanced non–small cell lung cancer (NSCLC) for treatment with tyrosine kinase inhibitors (gefitinib or erlotinib), v-raf murine sarcoma viral oncogene homolog B1 (BRAF) mutations for selecting patients with advanced melanoma for treatment with anti-BRAF agents (vemurafenib and dabrafenib), and anaplastic lymphoma receptor tyrosine kinase (ALK) translocations for identifying patients with NSCLC likely to benefit from crizotinib.

SUMMARY
The availability of companion biomarkers should improve drug efficacy, decrease toxicity, and lead to a more individualized approach to cancer treatment.
Habitat distribution modeling reveals vegetation flammability and land use as drivers of wildfire in SW Patagonia
Authors: Paritsis Juan , Holz Andrés , Veblen Thomas T. , Kitzberger Thomas 
Published: May 2013

Despite important recent advances in modeling current and future global fire activity in relation to biophysical predictors there remain important uncertainties about finer‐scale spatial heterogeneity of fire and especially about human influences which are typically assessed at coarse‐spatial resolutions. The purpose of the current study is to quantify the influence of biophysical and anthropogenic variables on the spatial distribution of wildfire activity between 1984 and 2010 over an extensive southern Patagonian‐Andean region from ca. 43° to 53° S extending from coastal rainforests to xeric woodland and steppe.We used satellite imagery to map all detectable fires >5 ha from 1984 to 2010 in four study areas (each of 13,100 to 36,635 km2) and field checked 65 of these burns for accuracy of burned vegetation class and fire perimeters. Then, we used the MaxEnt modeling technique to assess the relationships of wildfire distributions to biophysical and human environmental variables in each of the four regions. The 232 fires >5 ha mapped in the four study areas accounted for an area of 1,314 km2indicating that at least 1.8% of the total area burned between 1984 and 2010. In general, areas with intermediate productivity levels (e.g., shrublands) have higher fire probability compared with areas of low and high productivity levels, such as steppe and wet forests, respectively. There is a marked contrast in the flammability of broad vegetation classes in determining fire activity at a regional scale, as well as a strong spatial relationship of wildfires to anthropogenic variables. The juxtaposition of fire‐resistant tall forests with fire‐prone shrublands and woodlands creates the potential for positive feedbacks from human‐set fires to gradually increase the flammability of extensive landscapes through repeated burning. Distance to roads and settlements were also strong predictors, suggesting that fire in all regions is ignition‐limited. However, these anthropogenic predictors influenced probability of fire differently among study regions depending on their main land‐use practices and their past and present socioeconomic contexts.
Toll‐Like Receptor 4 Expression in Trigeminal Neurons Is Increased During Ligature‐Induced Periodontitis in Rats
Authors: Vindiš Bojan , Gašperšič Rok , Skalerič Uroš , Kovačič Uroš 
Published: May 2013

Background: Periodontitis, activated by oral bacteria and orchestrated by innate immune response, is regulated by primary nociceptive neurons, which are generally considered to have small‐ to medium‐sized perikaryons. Bacterial byproducts (e.g., lipopolysaccharides) activate primary nociceptive neurons directly through Toll‐like receptors (TLRs). Therefore, this study aims to morphometrically characterize rat trigeminal neurons, which express TLR4, and to investigate the changes in the TLR4 expression in neurons during periodontal inflammation.Methods: Trigeminal neurons innervating gingivomucosa were identified by application of the retrograde tracer hydroxystilbamidine into the gingival sulcus of the maxillary molar in 14 rats. Periodontitis was induced by ligature around the same molar in seven rats. TLR4 expression was investigated by immunohistochemistry on paraffin sections of the trigeminal ganglia (TG). Semiquantitative method was used to identify the intensity of TLR4 expression.Results: In the control group without the ligatures, TLR4 was detected in 19% of the neurons in the maxillary region of TG and in 29% of neurons innervating gingivomucosa. Expression of TLR4 was more frequent and intensive in small‐ to medium‐sized neurons than in large‐sized neurons. One week after ligature‐induced periodontitis, the percentage of TLR4‐positive neurons in the maxillary region and among the neurons innervating inflamed gingivomucosa significantly increased statistically to 32% and 41%, respectively.Conclusions: TLR4 is predominantly, but not exclusively, expressed in smaller trigeminal nociceptive neurons in the rat. Experimental periodontitis upregulates TLR4 expression in the trigeminal neurons. The hypothesis that bacterial byproducts regulate the pathogenesis of periodontitis by activation of trigeminal nociceptors through TLR4 should be explored.
Soluble Triggering Receptor Expressed on Myeloid Cells 1 (sTREM‐1) in Gingival Crevicular Fluid: Association With Clinical and Microbiologic Parameters
Authors: Belibasakis Georgios N. , Öztürk Veli‐Özgen , Emingil Gulnur , Bostanci Nagihan 
Published: May 2013

Background: Soluble triggering receptor expressed on myeloid cells 1 (sTREM‐1) belongs to the immunoglobulin superfamily and is involved in amplification of the inflammatory response to bacterial infection. This cross‐sectional study aims to investigate the levels of sTREM‐1 in gingival crevicular fluid (GCF) of individuals without periodontitis and with chronic periodontitis (CP) or generalized aggressive periodontitis (GAgP) and their association with the levels of key periodontal pathogens in subgingival plaque.Methods: GCF and subgingival plaque samples were obtained from healthy sites of participants without periodontitis (n = 20) and periodontitis sites of patients with CP (n = 22) and GAgP (n = 20). sTREM‐1 levels in GCF were measured by enzyme‐linked immunosorbent assay. Porphyromonas gingivalis, Treponema denticola, Tannerella forsythia, and Aggregatibacter actinomycetemcomitans levels in subgingival plaque were analyzed by quantitative real‐time polymerase chain reaction.Results: sTREM‐1 levels in GCF were higher in CP and GAgP than healthy sites by 3.6‐ and 4.4‐fold, respectively, with no significant differences between the two forms of periodontitis. Moreover, sTREM‐1 levels in GCF were positively correlated with site‐specific clinical periodontal parameters and levels of P. gingivalis, T. denticola, and T. forsythia, but not A. actinomycetemcomitans, in subgingival plaque.Conclusion: Increased GCF levels of sTREM‐1 at diseased sites and their positive correlation with clinical and microbiologic parameters strengthen the association of this inflammatory marker with periodontitis.
Validation of Digital Rock Physics Based Water-Oil Capillary Pressure and Saturation Exponents in Super Giant Carbonate Reservoirs
Authors: Kalam Zubair , Gibrata Muhammad , Al Hammadi Mohammad , Mock Aex , Lopez Oliver 
Published: May 2013

Abstract
Digital Rock Physics (DRP) has progressed at a rapid speed since the first pore network models were developed. DRP has now evolved in to a new discipline and essentially involves use of X-ray CT scanning in micro and Nano-CT to capture the 3D network structure of representative reservoir rock types. The proliferation of the technique with powerful computers and robust network modeling means one can rapidly determine various Special Core Analysis (SCAL) properties that form the basis of reservoir characterization parameters: porosity, permeability, formation factor, cementation and saturation exponents, capillary pressure, relative permeability and elastic properties.
A comprehensive DRP based validation study was performed on reservoir core plugs which had undergone rigorous Petrophysical SCAL at representative pseudo reservoir conditions. The objective was to assess the use of DRP in determining such data, and quantifying the relevant uncertainties. The plugs were chosen from two super giant carbonate reservoirs in the Middle East. The laboratory tests comprised cementation exponent ‘m’ at a range of pressures, water-oil capillary pressure (Pc) and electrical resistivity index (RI) tests at reservoir temperature and reservoir overburden pressure using specially designed Porous Plates.
Capillary pressure under primary drainage and imbibition conditions, replicating reservoir conditions were established using multi-phase flow simulations on the pore network representation of the 3D rock model. Similarly, the cementation exponent ‘m’ was calculated using a solution of the Laplace equation with charge conservation; the equations were solved using a random walk algorithm. DRP based primary drainage and imbibition saturation exponents ‘n’ were also computed for cores samples of different reservoir rock types. The results were then compared to measured SCAL data, and validation criteria established along with possible uncertainties. DRP is extremely promising in generating fairly accurate SCAL parameters very fast from existing cores.
Extended Long-Term (5 Years) Outcomes of Triangle Tilt Surgery in Obstetric Brachial Plexus Injury
Authors: Nath Rahul K , Somasundaram Chandra 
Published: May 2013

Objective:
We evaluated the "extended" long-term (5 years) functional outcomes in obstetric brachial plexus injury (OBPI) patients, who underwent triangle tilt surgery between February 2005 and January 2008.

Methods:
Twenty two children (9 girls and 13 boys, mean age at surgery was 5.8 years; ranging 2.1-11.8 years old), who initially presented with medial rotation contracture and scapula deformity secondary to obstetric brachial plexus injury were included in this study. Functional movements were evaluated pre-operatively, and 5 years following triangle tilt surgery by modified Mallet scale.

Results:
Here, we report long-term (5 years) follow-up of triangle tilt surgery for 22 OBPI patients. Upper extremity functional movements such as, external rotation (2.5±0.6 to 4.1±0.8, p<0.0001), hand-to-spine (2.6±0.6 to 3.4±1.1, p<0.005), hand-to-neck (2.7±0.7 to 4.3±0.7, p<0.0001), hand-to-mouth (2.3±0.9 (92º±33) to 4.2±0.5 (21º±16), p<0.0001), and supination (2.6±1.1 (-8.2º ±51) to 4.1±0.7 (61±32)) were significantly improved (p<0.0001), and maintained over the extended long-term (5 years). Total modified Mallet functional score was also shown to improve from 14.1±2.7 to 20.3±2.5.

Conclusions:
The triangle tilt surgery improved all shoulder functions significantly, and maintained over the extended long-term (5 years) in these patients.
Fat Distribution and Glucose Intolerance Among Greenland Inuit
Authors: Jørgensen Marit Eika , Borch-Johnsen Knut , Stolk Ronald , Bjerregaard Peter 
Published: May 2013

OBJECTIVE
A high amount of subcutaneous fat is suggested to explain the observation of lower obesity-associated metabolic risk among Inuit than among Europeans. We examined the association between measures of obesity (visceral adipose tissue [VAT], subcutaneous adipose tissue [SAT], BMI, waist circumference [WC], and percentage of body fat) and the indices of glucose metabolism (fasting and 2-h glucose levels, insulin resistance per homeostasis model assessment [HOMA-IR], and the insulin sensitivity index [ISI0,120]) among Greenland Inuit.

RESEARCH DESIGN AND METHODS
A total of 3,108 adult Inuit participated in a population-based study. The examination included a 75-g oral glucose tolerance test and anthropometric measurements. VAT and SAT were measured by ultrasound according to a validated protocol. Information on sociodemographic characteristics and health behaviors was obtained by interview.

RESULTS
Mean SATs were 1.8 and 3.5 cm in men and women, respectively. Mean VATs were 7.0 and 6.3 cm in men and women, respectively. The total prevalence of type 2 diabetes was 9%. Percentage of body fat generally was most strongly associated with all outcomes. Both SAT and VAT were significantly associated with glucose intolerance, fasting and 2-h plasma glucose levels, HOMA-IR, and ISI0,120. VAT was more strongly associated with all outcomes than was SAT. After further adjustment for BMI or WC, VAT was associated with glucose intolerance and insulin resistance, whereas there was a trend toward a negative or no association with SAT.

CONCLUSIONS
High mean values of SAT may to a large extent explain the high WC in Inuit populations, and this is suggested to contribute to the lower observed metabolic risk for a given level of obesity.
Comparison of Corneal Flap Morphology Using AS-OCT in LASIK With the WaveLight FS200 Femtosecond Laser Versus a Mechanical Microkeratome
Authors: Zhang Yu , Chen Yue-guo , Xia Ying-jie 
Published: May 2013

PURPOSE:
To evaluate and compare the thickness and the morphology of femtosecond and mechanical microkeratome LASIK flaps using anterior segment optical coherence tomography (AS-OCT).

METHODS:
Bilateral LASIK was performed in 132 eyes from 61 myopic patients. Flaps were created in 72 eyes using the WaveLight FS200 femtosecond laser (Wave-Light GmbH, Erlangen, Germany) and in 50 eyes using the Moria microkeratome (Moria SA, Antony, France). AS-OCT was used 1 week postoperatively to evaluate the thickness of 17 points across each flap, which were 0, 2, and 3.5 mm to the corneal vertex on the horizontal, vertical, 45°, and 135° meridians.

RESULTS:

The mean central flap thickness was 105.53 ± 5.86
μ
m in the WaveLight group and 132.96 ± 13.91
μ
m in the Moria group (
P
< .001). The difference between the achieved and the intended flap thickness (accuracy) was 6.17 ± 3.98 and 23.60 ± 12.64 μm, respectively (
P
< .001). The standard deviation within individual flap (uniformity) was smaller in the WaveLight group. The symmetry and regularity were also better in the WaveLight group. Flap morphology showed a more regular planar shape in the WaveLight group and a meniscus shape in the Moria group.

CONCLUSIONS:
AS-OCT showed that the flaps created by the WaveLight femtosecond laser were more accurate, reproducible, and uniform than those created by the Moria microkeratome.

[
J Refract Surg.
2013;29(5):320–324.]
Biological and Biomechanical Responses to Traditional Epithelium-Off and Transepithelial Riboflavin-UVA CXL Techniques in Rabbits
Authors: Armstrong Brian K. , Lin Michelle P. , Ford Matthew R. , Santhiago Marcony R. , Singh Vivek , Grossman Gregory H. , Agrawal Vandana , Roy Abhijit Sinha , Butler Robert S. , Dupps William J. , Wilson Steven E. 
Published: May 2013

PURPOSE:
To compare the biological effects of riboflavin-ultraviolet A (UVA) corneal cross-linking (CXL) performed with a traditional epithelium-off method to several transepithelial methods in a rabbit model. Preliminary experiments on biomechanical rigidity were also performed.

METHODS:
Four treatment groups were included: (1) standard epithelium-off, (2) tetracaine transepithelial, (3) benzal-konium chloride-ethylenediaminetetraacetic acid (BKC-EDTA) transepithelial, and (4) femtosecond laser-assisted transepithelial riboflavin-UVA CXL. Six eyes from each treatment group and the untreated control group were analyzed at 24 hours and 2 months after treatment in wound healing studies. The TUNEL assay was performed to detect the extent of stromal cell death. Optical density was measured with a Scheimpflug analyzer. The corneal stiffening effect was quantitated in three eyes from each group using optical coherence elastography performed 2 months after treatments.

RESULTS:

Twenty-four hours after CXL, stromal cell death extended full corneal thickness with both standard epithelium-off CXL and femtosecond laser-assisted CXL, but only approximately one-third stromal depth after BKC-EDTA transepithelial CXL. Negligible stromal cell death was detected with tetracaine transepithelial CXL. Cell death results were statistically different between the BKC-EDTA transepithelial CXL and standard epithelium-off CXL groups (
P
< .0001). Significant corneal opacity differences were noted. Standard epithelium-off CXL had the greatest density and tetracaine transepithelial CXL had the least density compared to the control group after treatment. As measured with optical coherence elastography, a trend toward greater mean stiffening was observed with BKC-EDTA transepithelial CXL than with epithelium-off CXL, femtosecond laser-assisted CXL, or tetracaine transepithelial CXL, but the result did not reach statistical significance. All of the CXL treatment groups exhibited significantly smaller variance of stiffness compared to the control group.

CONCLUSION:
In the rabbit model, BKC-EDTA transepithelial CXL produced less stromal cell death and less risk of endothelial cell damage than standard epithelium-off CXL or femtosecond laser-assisted CXL. Additional study is needed to determine whether biomechanical stiffness is significantly different between the epithelium-off CXL and transepithelial CXL groups.

[
J Refract Surg.
2013;29(5):332–341.]