bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ultrasound‐guided approach to the paravertebral space for catheter insertion in infants and children
Authors: Boretsky Karen , Visoiu Mihaela , Bigeleisen Paul 
Published: July 2013

SummaryBackgroundParavertebral perineural blocks are used to prevent pain in the thoracoabdominal dermatomes. Traditionally, a landmark‐based technique is used in children, while ultrasound‐guided (UG) techniques are being employed in adult patients.ObjectiveTo describe an UG technique for placement of thoracic paravertebral nerve block (TPVNB) catheters in pediatric patients.MethodsRetrospective chart review of a series of 22 pediatric patients' ages 6 months to 17 years with weights from 6.25 kg to 135 kg using a transverse in‐plane technique. Catheters were placed both bilateral and unilateral for a variety of thoracic and abdominal procedures.A linear ultrasound transducer was used in all cases with frequency of oscillation and transducer length chosen based on individual patient characteristics of age, weight, and BMI.ResultsThe median pain scores at 12, 24, 36, and 48 h were 1.2 (interquartile range, 4.5), 0.84 (interquartile range 3.0), 1.6 (interquartile range 2.9), and 0.83 (interquartile range 1.74), respectively. The median dose of opioid expressed as morphine equivalents consumed during the first 24 h after surgery was 0.14 mg·kg−1 (interquartile range, 0.78 mg·kg−1) and from 24 to 48 h the median dose was 0.11 mg·kg−1 (interquartile range 0.44 mg·kg−1). No complications were noted, and catheters were left an average of 3 days with a range of 1–5 days with good pain relief.ConclusionThis technical description demonstrates the feasibility of placing PVNB catheters using a transverse in‐line ultrasound‐guided technique in a wide range of pediatric patients.
Molecular Typing of CTX-M-Producing Escherichia coli Isolates from Environmental Water, Swine Feces, Specimens from Healthy Humans, and Human Patients
Authors: Hu Yan-Yan , Cai Jia-Chang , Zhou Hong-Wei , Chi Dan , Zhang Xiao-Fei , Chen Wei-Liang , Zhang Rong , Chen Gong-Xiang 
Published: July 2013

ABSTRACT

CTX-M-producing
Escherichia coli
is the predominant type of extended-spectrum β-lactamase (ESBL)-producing
E. coli
worldwide. In this study, molecular typing was conducted for 139 CTX-M-producing
E. coli
isolates, phenotypically positive for ESBLs, isolated from environmental water, swine, healthy humans, and hospitalized patients in Hangzhou, China. The antibiotic resistance profiles of the isolates for the cephalosporins and fluoroquinolones were determined. The isolates showed 100% resistance to cefotaxime and ceftriaxone while maintaining relatively high susceptibility to cefoxitin, cefepime, and ceftazidime. A total of 61.9% (86/139) of the isolates, regardless of origin, showed high resistance to fluoroquinolones. PCRs and DNA sequencing indicated that
bla
CTX-M-14
was the most prevalent CTX-M-9 group gene and that
bla
CTX-M-15
and
bla
CTX-M-55
were the dominant CTX-M-1 group genes. Isolates from all sources with CTX-M types belonging to the CTX-M-1 or CTX-M-9 group were most frequently associated with epidemics. Molecular homology analysis of the isolates, conducted by phylogenetic grouping, pulsed-field gel electrophoresis (PFGE), and multilocus sequence typing (MLST), demonstrated that the dominant clones belonged to B2-ST131, D-ST648, D-ST38, or A-CC10. These four sequence types (STs) were discovered in
E. coli
isolates both from humans and from environmental water, suggesting frequent and continuous intercompartment transmission between humans and the aquatic environment. Seven novel sequence types were identified in the current study. In conclusion, this study is the first to report the molecular homology analysis of CTX-M-producing
E. coli
isolates collected from water, swine, and healthy and hospitalized humans, suggesting that pathogens in the environment might originate both from humans and from animals.
Antimicrobial Resistance in Indicator Escherichia coli Isolates from Free-Ranging Livestock and Sympatric Wild Ungulates in a Natural Environment (Northeastern Spain)
Authors: Navarro-Gonzalez N. , Porrero M. C. , Mentaberre G. , Serrano E. , Mateos A. , Domínguez L. , Lavín S. 
Published: July 2013

ABSTRACT

Antimicrobial resistance was assessed in indicator
Escherichia coli
isolates from free-ranging livestock and sympatric wild boar (
Sus scrofa
) and Iberian ibex (
Capra pyrenaica
) in a National Game Reserve in northeastern Spain. The frequency of antimicrobial resistance was low (0% to 7.9%). However, resistance to an extended-spectrum cephalosporin and fluoroquinolones was detected.
Functional Characterization of Core Components of the Bacillus subtilis Cyclic-Di-GMP Signaling Pathway
Authors: Gao Xiaohui , Mukherjee Sampriti , Matthews Paige M. , Hammad Loubna A. , Kearns Daniel B. , Dann Charles E. 
Published: July 2013

ABSTRACT

Bis-(3′-5′)-cyclic dimeric GMP (c-di-GMP) is an intracellular second messenger that regulates adaptation processes, including biofilm formation, motility, and virulence in Gram-negative bacteria. In this study, we have characterized the core components of a c-di-GMP signaling pathway in the model Gram-positive bacterium
Bacillus subtilis
. Specifically, we have directly identified and characterized three active
d
i
g
uanylate
c
yclases, DgcP, DgcK, and DgcW (formerly YtrP, YhcK, and YkoW, respectively), one active c-di-GMP
p
hospho
d
i
e
sterase, PdeH (formerly YuxH), and a cyclic-
d
i
g
uanylate (c-di-GMP)
r
eceptor, DgrA (formerly YpfA). Furthermore, elevation of c-di-GMP levels in
B. subtilis
led to inhibition of swarming motility, whereas biofilm formation was unaffected. Our work establishes paradigms for Gram-positive c-di-GMP signaling, and we have shown that the concise signaling system identified in
B. subtilis
serves as a powerful heterologous host for the study of c-di-GMP enzymes from bacteria predicted to possess larger, more-complex signaling systems.
Integrated flat detector CT and live fluoroscopic-guided external ventricular drain placement within the neuroangiography suite
Authors: Fiorella David , Peeling Lissa , Denice Christine M , Sarmiento Marily , Woo Henry H 
Published: July 2013

PurposeTo demonstrate the feasibility of the application of integrated flat detector (FD) CT and fluoroscopic guidance (iGuide) for the placement of external ventricular drains (EVD) within the neuroangiography suite.MethodsA retrospective review of a prospectively maintained endovascular database identified six patients who underwent EVD placement using iGuide. Patient characteristics, operator, number of passes, accuracy of placement, immediate and delayed periprocedural complications and radiation exposure were assessed.ResultsFive patients with subarachnoid hemorrhage and one patient with a large cerebellar infarct (average age 45.5 years (range 39–53), four women) underwent EVD placement within the angiography suite using iGuide. Four procedures were performed by a neuroradiologist and two by a neurosurgeon. All catheters were placed with a single pass and all terminated within the frontal horn of the ipsilateral lateral ventricle. No parenchymal or intraventricular hemorrhages were encountered after catheter placement. No patients experienced any immediate or delayed periprocedural complications. Radiation exposure related to the FD CTs required for placement was 593.7 mGy (range 539–673).ConclusionsEVD placement under combined CT and fluoroscopic control within the neuroangiography suite is feasible. The technique predictably allows optimized EVD catheter placement with a single pass. We propose that this technique could improve the accuracy, and potentially reduce the complications, of EVD insertion in cerebrovascular patients.
Aerosol Replenishment and Cloud Morphology: A VOCALS Example
Authors: Jiang Qingfang , Wang Shouping 
Published: July 2013

Abstract
The impact of aerosol replenishment in a stratocumulus-topped boundary layer (STBL) on cloud morphology and albedo is examined using a large-eddy simulation (LES) model in conjunction with a prey–predator-type dynamical model following Koren and Feingold. In both the LES and the prey–predator models, the aerosol replenishment is represented as a relaxation term toward an ambient aerosol concentration with a time scale . The LESs suggest the existence of three distinct cloud regimes corresponding to different aerosol relaxation times. Specifically, for a small , the simulations are characterized by a large aerosol concentration, weak precipitation, relatively thick cloud depth, and closed cells. For a moderate , the simulated clouds exhibit open cellular patterns, in accordance with low aerosol concentration and moderate precipitation that oscillates in time. For a large , the aerosol may be depleted by intense drizzling and accordingly the cloud disappears. The critical aerosol relaxation times that separate these regimes vary with the ambient aerosol number concentration and cloud depth. Solutions from the low-order dynamical model with parameters relevant to the LESs are in general consistent with the LES results and provide further insight into the interplay among clouds, aerosol, and precipitation.
Construction of small RNA-mediated gene regulatory networks in the roots of rice (Oryza sativa)
Authors: Ma Xiaoxia , Shao Chaogang , Wang Huizhong , Jin Yongfeng , Meng Yijun 
Published: July 2013

Abstract

Background
The root systems play essential roles for plants to anchorage to the soil, and to exploit the mineral and water resources. The molecular mechanisms underlying root development have been extensively studied to improve root system architecture, especially for the crops. Several microRNA (miRNA) families have been demonstrated to be involved in plant root development. However, whether the other small RNA (sRNA) species, which occupy a dominant portion of the plant endogenous sRNA population, possess potential roles in root development remains unclear.

Results
In this study, by using sRNA high-throughput sequencing data, we made a comparison of the sRNA accumulation levels between the rice root tips and the whole roots. The sRNAs highly accumulated in the root tips and in the whole roots were extracted respectively. After Argonaute 1 (AGO1) enrichment analysis, the sRNAs with great potential of performing target cleavages were included for target prediction and degradome sequencing data-based validation. As a result, lists of the targets regulated by the AGO1-enriched sRNAs were obtained for both the root tips and the whole roots. Further evidences were identified from microarray data of the target genes to support some of the sRNA—target interactions. Specifically, the expression patterns of certain target genes in the root tips and the whole roots were contrary to those of the regulating sRNAs. Besides, several targets were indicated to play important roles in root development based on literature mining.

Conclusions
Taken together, the regulatory networks mediated by the sRNAs highly accumulated in the root tips or in the whole roots could advance our current understanding of the sRNA-involved molecular mechanisms underlying rice root development. And, the sRNA—target lists could serve as the basis for further functional investigations.
Twenty-one new sequence markers for population genetics, species delimitation and phylogenetics in wall lizards (Podarcis spp.)
Authors: Pereira Carolina , Couto Alvarina , Luís Carla , Costa Diogo , Mourão Sofia , Pinho Catarina 
Published: July 2013

Abstract

Background
Wall lizards of genus Podarcis are abundant and conspicuous reptiles inhabiting Europe and North Africa. In recent years, they have become a popular lizard model for phylogeographical and evolutionary ecology studies. However a lack of suitable nuclear markers currently presents a limitation on analyses of molecular evolution within this genus. We address this limitation by developing twenty-one new primer pairs for polymerase chain reaction (PCR) amplification and sequencing of anonymous sequence markers in Podarcis vaucheri and performed an assay of their cross-amplification and polymorphism levels in two closely- (P. bocagei and P. liolepis) and two distantly-related (P. muralis and P. tiliguerta) congeners.

Findings
Cross-amplification and sequencing was straightforward among members of the Iberian and North-African group within genus Podarcis (which includes P. vaucheri), and somewhat less successful in species belonging to other groups (one and four loci out of 21 failed to amplify in P. muralis and P. tiliguerta, respectively, and overall success rates were lower). Nucleotide diversity for the five species examined ranged from 0.35% to 3.5%, with an average of 1.5% across all loci. Insertion and deletion polymorphisms were found in all but three loci.

Conclusions
Given the high cross-amplification rates, these markers constitute a valuable addition to set of genomic resources available for Podarcis, especially in studies dealing with phylogenetics, species delimitation, population genetics and phylogeography.
Myeloperoxidase modulates human platelet aggregation via actin cytoskeleton reorganization and store-operated calcium entry
Authors: Gorudko Irina V. , Sokolov Alexey V. , Shamova Ekaterina V. , Grudinina Natalia A. , Drozd Elizaveta S. , Shishlo Ludmila M. , Grigorieva Daria V. , Bushuk Sergey B. , Bushuk Boris A. , Chizhik Sergey A. , Cherenkevich Sergey N. , Vasilyev Vadim B. , Panasenko Oleg M. 
Published: July 2013

Summary
Myeloperoxidase (MPO) is a heme-containing enzyme released from activated leukocytes into the extracellular space during inflammation. Its main function is the production of hypohalous acids that are potent oxidants. MPO can also modulate cell signaling and inflammatory responses independently of its enzymatic activity. Because MPO is regarded as an important risk factor for cardiovascular diseases associated with increased platelet activity, we studied the effects of MPO on human platelet functional properties. Laser scanning confocal microscopy was used to reveal carbohydrate-independent MPO binding to human platelet membrane. Adding MPO to platelets did not activate their aggregation under basal conditions (without agonist). In contrast, MPO augmented agonist-induced platelet aggregation, which was not prevented by MPO enzymatic activity inhibitors. It was found that exposure of platelets to MPO leads to actin cytoskeleton reorganization and an increase in their elasticity. Furthermore, MPO evoked a rise in cytosolic Ca2+ through enhancement of store-operated Ca2+ entry (SOCE). Together, these findings indicate that MPO is not a direct agonist but rather a mediator that binds to human platelets, induces actin cytoskeleton reorganization and affects the mechanical stiffness of human platelets, resulting in potentiating SOCE and agonist-induced human platelet aggregation. Therefore, an increased activity of platelets in vascular disease can, at least partly, be provided by MPO elevated concentrations.
Zeolites in Mafic Pyroclastic Rocks from the Sandikli-Afyonkarahisar Region, Turkey
Authors: Ozpinar Yahya , Semiz Baris , Schroeder Paul A. 
Published: July 2013

AbstractGeologic mapping and crystal-chemical analysis of Middle-Upper Miocene volcanics in the Sandıklı-Afyonkarahisar region of Turkey, coupled with published zeolite analyses has revealed that western Turkey hosts unique zeolitic mineral assemblages with distinct paragenetic sequences. The present investigation focused on pyroclastic deposits, including low to intermediate potassic trachytic/trachyandesitic tuffs (LPT) and high potassic tephriphonolitic, tephritic, and trachybasaltic tuffs (HPT), each of which contains various styles of zeolites. Optical petrography, X-ray powder diffraction, and chemical analyses have revealed varying degrees of lithification, probably related to differences in initial emplacement temperature, depositional mechanism and thickness, chilling rate, and extent of mafic composition. Zeolitization was further influenced by meteoric flushing in a hydrologically open system. Chabazite in the LPT from the Selçik area occurs extensively as coatings and infillings of pores. Phillipsite in the HPT found in the Ballık, Küfeke, and Ömerkuyu areas dominates the assemblage and is accompanied by chabazite and minor amounts of analcime. Analcime was probably generated by alteration of leucite which is found as a pyrogene mineral. Alkali zeolites or Ca-bearing zeolites formed as a consequence of the addition of Ca and/or the removal of Na (i.e. dissolution of analcime). The paragenetic sequence may be described as: analcime/phillipsite → chabazite → calcite. The characterization of these assemblages may lead to better exploitation strategies for natural zeolitic resources in the region.
Structure Determination of Trimethylsulfoxonium-Exchanged Vermiculite
Authors: Johns Candice A. , Martos-Villa Rubén , Guggenheim Stephen , Sainz-Díaz C. Ignacio 
Published: July 2013

AbstractThe structure of trimethylsulfoxonium-exchanged vermiculite has been examined to compare it with other onium-exchanged structures, such as tetramethylammonium- and tetramethylphosphonium-exchanged vermiculite. The three organic cations are tetrahedral in shape, but trimethylsulfoxonium [(CH3)3SO+] has an oxygen atom replacing a methyl group at one apex. This study describes the effect this substitution and the larger S atom have on the site location in the interlayer and the effect on the vermiculite 2:1 layer. These clay minerals may be commercially useful as adsorbents.Na-exchanged crystals of vermiculite from Santa Olalla, Spain, were intercalated with trimethylsulfoxonium [Me3SO+ = (CH3)3SO+] molecules by refluxing in an aqueous 0.25 M trimethylsulfoxonium iodide solution at 80°C for 14 days. The resulting Me3SO+-exchanged vermiculite crystals were studied by single-crystal, X-ray diffraction methods and by computer modeling (density functional theory). Cell parameters are a = 5.349(2), b = 9.270(3), c = 13.825(8) Å, and β = 97.40(4)°, the space group is C2/m, and the polytype is 1M. Refinement results (R = 0.073, wR = 0.080) show that in the average structure of C2/m, the S atoms of the Me3SO+ molecules form two partially occupied planes [2.066(2) Å from each basal oxygen plane] between the 2:1 layers, and the S atoms show considerable positional disorder. The O atom of the Me3SO+ molecule occurs in the central plane of the interlayer, as far away from each 2:1 layer as possible. In projection down the c* axis, the Me3SO+ molecule resides within the center of the silicate rings from each adjacent 2:1 layer. In the ideal (static) model of the Me3SO+-exchanged vermiculite structure, the Me3SO+ molecule is oriented such that two methyl groups point toward charge-deficient bridging oxygen atoms of the basal plane; thus, the organic pillars charge compensate the bridging oxygen atoms of the 2:1 layer that are charge deficient. In projection, the oxygen atom of the Me3SO+ molecule projects over a tetrahedron containing Si. Computer modeling showed that if H2O is not included in the model, the Me3SO+ molecule (S and O atoms) is in the center of the interlayer, but with the addition of randomly placed H2O, two partially occupied planes similar to the X-ray derived model are formed.
Application of BRAF, NRAS, KRAS mutations as markers for the detection of papillary thyroid cancer from FNAB specimens by pyrosequencing analysis
Authors: Park Seo-Jin , Sun Je Young Hannah , Hong Kyungran , Kwak Jin Young , Kim Eun-Kyung , Chung Woung Youn , Choi Jong Rak 
Published: July 2013

Abstract

Background:
BRAF
V600E, the most common BRAF gene mutation, is detected in approximately 50% of sporadic papillary thyroid carcinoma (PTC) and may be associated with triggering tumorigenesis of PTC. The aim of our study was to discover additional mutations to increase the diagnostic performance of molecular tests in screening for thyroid cancer from fine needle aspiration biopsy (FNAB) specimens.

Methods: DNA was extracted from 120 freshly obtained FNAB specimens selected according to cytopathology grades of the Bethesda system. A conventional BRAF
V600E test was carried out with real-time PCR, and further mutation screening for BRAF mutations in codons 464, 466, 469, NRAS and KRAS codons 12/13 and 61 was done by pyrosequencing. Histopathology reports were reviewed for those who underwent thyroidectomy (n=83).

Results: The real-time PCR method detected 45 BRAF
V600E- positive cases whereas pyrosequencing detected 30 cases. Additional BRAF (n=4), NRAS (n=11) and KRAS (n=3) mutations were detected in 17 cases (one overlapping BRAF and NRAS mutation). Among 11 NRAS-mutated cases, eight were confirmed as PTC and one as FVPTC on histopathology reports. Five PTC-confirmed cases with BRAF
V600E mutation showed additional mutations, all of which were NRAS mutations.

Discussion: Despite the higher sensitivity of real-time PCR for detecting BRAF
V600E mutations, pyrosequencing easily detected additional point mutations. NRAS mutations were the most prevalently identified additional mutations and were highly associated with malignancy. In conclusion, our findings demonstrate that additional mutations identified by pyrosequencing may help in the pre-operative process in determining the possibility of malignancy and further studies on the occurrence of simultaneous mutations of BRAF, KRAS and NRAS may be warranted.
Expression and characterisation of fully posttranslationally modified cellular prion protein in Pichia pastoris
Authors: Marbach Jendrik , Zentis Peter , Ellinger Philipp , Müller Henrik , Birkmann Eva 
Published: July 2013

Abstract
Prion diseases are fatal neurodegenerative diseases which occur as sporadic, genetic, and transmissible disorders. A molecular hallmark of prion diseases is the conformational conversion of the host-encoded cellular form of the prion protein (PrPC) into its misfolded pathogenic isoform (PrPSc). PrPSc is the main component of the pathological and infectious prion agent. The study of the conversion mechanism from PrPC to PrPSc is a major field in prion research. PrPC is glycosylated and attached to the plasma membrane via its glycosyl phosphatidyl inositol (GPI)-anchor. In this study we established and characterised the expression of fully posttranslationally modified mammalian Syrian golden hamster PrPC in the yeast Pichia pastoris using native PrPC-specific N- and C-terminal signal sequences. In vivo as well as in vitro-studies demonstrated that the signal sequences controlled posttranslational processing and trafficking of native PrPC, resulting in PrPC localised in the plasma membrane of P. pastoris. In addition, the glycosylation pattern of native PrPC could be confirmed.
Monitoring the Intraday Volatility Pattern
Authors: Gabrys Robertas , Hörmann Siegfried , Kokoszka Piotr 
Published: July 2013

AbstractA functional time series consists of curves, typically one curve per day. The most important parameter of such a series is the mean curve. We propose two methods of detecting a change in the mean function of a functional time series. The change is detected on line, as new functional observations arrive. The general methodology is motivated by, and applied to, the detection of a change in the mean intraday volatility pattern. The methodology is asymptotically justified by applying a new notion of weak dependence for functional time series. It is calibrated and validated by simulations based on real intraday volatility curves.