bluuebunny/crossref_metadata_2025_split huggingface dataset:
Monitoring triplet state dynamics with fluorescence correlation spectroscopy: Bias and correction
Authors: Schönle Andreas , Von Middendorff Claas , Ringemann Christian , Hell Stefan W. , Eggeling Christian 
Published: April 2014

ABSTRACTA marker's dark triplet state is of great importance in fluorescence microscopy: It serves as a means to switch off fluorescent markers and is thus the enabling element for several super‐resolution methods. On the other hand, intersystem‐crossing to the electronic dark triplet state strongly reduces the fluorescence yield in conventional fluorescence microscopy. The ability to determine the kinetic parameters of transitions into the triplet state is thus of great importance and because fluorescence correlation spectroscopy (FCS) can be applied without disturbing the system under study, it is one of the preferred methods to do so. However, conventional FCS observations of triplet dynamics suffer from bias due to the spatially inhomogeneous irradiance profile of the excitation laser. Herein, we present a novel method to correct this bias and verify it by analyzing both Monte Carlo simulated and experimental data of the organic dye Rhodamine 110 in aqueous solution for both continuous‐wave and pulsed excitation. Importantly, our approach can be readily generalized to most other FCS experiments that determine intensity dependent kinetic parameters. Microsc. Res. Tech. 77:528–536, 2014. © 2014 Wiley Periodicals, Inc.
The development of a gridded weather typing classification scheme
Authors: Lee Cameron C. 
Published: April 2014

ABSTRACTGridded reanalysis datasets have proven quite useful for a broad range of synoptic climatological analyses, especially those utilizing a map‐pattern classification approach. However, their use in broad‐scale, surface weather typing classifications and applications have not yet been explored. This research details the development of such a gridded weather typing classification (GWTC) scheme using North American Regional Reanalysis data for 1979–2010 for the continental United States. Utilizing eight‐times daily observations of six surface variables, the GWTC categorizes the daily surface weather of 2070 locations into one of 11 discrete weather types – nine core types and two transitional types (TRs) – that remain consistent throughout the domain. Due to the use of an automated deseasonalized z‐score initial typing procedure, the character of each type is both geographically and seasonally relative, allowing each core weather type to occur at every location, at any time of the year. Diagnostic statistics reveal a high degree of spatial cohesion among the weather types classified at neighbouring locations, along with an effective partitioning of climate variability into these 11 weather types. Daily maps of the spatial distribution of GWTC weather types across the United States correspond well to traditional surface weather maps, and comparisons of the GWTC with the Spatial Synoptic Classification are also favourable. While the potential future utility of the classification is expected to be primarily for the resultant calendars of daily weather types at specific locations, the automation of the methodology allows the classification to be easily repeatable, and therefore, easily transportable to other locations, atmospheric levels and datasets, including general circulation models. The enhanced spatial resolution of the GWTC may allow for new applications of surface weather typing classifications in mountainous and rural areas not well represented by weather stations.
Gas chromatographic detection of some nitro explosive compounds in soil samples after solid‐phase microextraction with carbon ceramic copper nanoparticle fibers
Authors: Farhadi Khalil , Bochani Shayesteh , Hatami Mehdi , Molaei Rahim , Pirkharrati Hossein 
Published: April 2014

In this research, a new solid‐phase microextraction fiber based on carbon ceramic composites with copper nanoparticles followed by gas chromatography with flame ionization detection was applied for the extraction and determination of some nitro explosive compounds in soil samples. The proposed method provides an overview of trends related to synthesis of solid‐phase microextraction sorbents and their applications in preconcentration and determination of nitro explosives. The sorbents were prepared by mixing of copper nanoparticles with a ceramic composite produced by mixture of methyltrimethoxysilane, graphite, methanol, and hydrochloric acid. The prepared sorbents were coated on copper wires by dip‐coating method. The prepared nanocomposites were evaluated statistically and provided better limits of detection than the pure carbon ceramic. The limit of detection of the proposed method was 0.6 μg/g with a linear response over the concentration range of 2–160 μg/g and square of correlation coefficient >0.992. The new proposed fiber has been demonstrated to be a suitable, inexpensive, and sensitive candidate for extraction of nitro explosive compounds in contaminated soil samples. The constructed fiber can be used more than 100 times without the need for surface generation.
The EQ‐5D: A new tool for studying clinical outcomes in chronic rhinosinusitis
Authors: Remenschneider Aaron K. , D'Amico Laura , Gray Stacey T. , Holbrook Eric H. , Gliklich Richard E. , Metson Ralph 
Published: April 2014

Objectives/HypothesisTo describe the role and applicability of the EuroQol 5‐Dimension, 5‐Level (EQ‐5D‐5L) questionnaire for the assessment of general health‐related quality of life in patients with chronic rhinosinusitis.Study DesignProspective cohort study.MethodsThe EQ‐5D‐5L was administered to 462 patients with refractory chronic rhinosinusitis before and 3 months after sinus surgery. Preoperative and postoperative scores across each of five health dimensions were analyzed and the results compared to those obtained from two widely used chronic rhinosinusitis outcomes instruments: the Chronic Sinusitis Survey (CSS) and SinoNasal Outcomes Test‐22 (SNOT‐22).ResultsThree hundred and fifty patients completed the five questions and visual analog scale (VAS) of the EQ‐5D at baseline and at 3 months for a response rate of 75.8%. There were no incomplete questionnaires. The frequency of patients reporting problems in the EQ‐5D domains of pain/discomfort, anxiety/depression, and usual activities decreased following sinus surgery (74.3% vs. 34.4%, 48.6% vs. 31.4%, and 30.6% vs. 19.4%, respectively; all P < 0.001). The domains of mobility and self‐care did not demonstrate statistically significant change. EQ‐5D VAS (standard deviation) improved from 73.4 (16.9) before surgery to 82.0 (14.4) after surgery (P < 0.001). Preoperative VAS correlated with SNOT‐22 scores (Pearson coefficient of 0.50; P < 0.01). Postoperative change in VAS and SNOT‐22 scores demonstrated moderate correlation (Pearson coefficient of 0.36, P < 0.01).ConclusionThe EQ‐5D is a general health measure with sensitivity to clinical change in rhinosinusitis that support its use for monitoring patient outcomes. The limited response burden and ability to directly calculate health utility make it an attractive tool for rhinosinusitis outcomes research.Level of Evidence2c. Laryngoscope, 125:7–15, 2015
Changing trends of speech outcomes after total laryngectomy in the 21st century: A single‐center study
Authors: Moon Seo , Raffa Francesca , Ojo Rosemary , Landera Mario A. , Weed Donald T. , Sargi Zouka , Lundy Donna 
Published: April 2014

Objectives/HypothesisTo describe the speech rehabilitation outcomes of patients undergoing total laryngectomy (TL) in the 21st century.Study DesignRetrospective chart review.SettingTertiary academic centerSubjects and MethodsRetrospective review of 167 patients who underwent TL from June 2000 to February 2012. Demographics, disease variables, and surgical factors were reviewed. Primary alaryngeal speech modality, speech outcome, and tracheoesophageal puncture (TEP) complication rates were assessed.ResultsOverall TEP speech success rate (primary or secondary) was 72%. Overall TEP speech success rate was 76% for those with primary TEP and was 68% for those with secondary TEP. TEP speech success rates at first, second, and beyond second year were 75%, 72%, and 70%, respectively. Success rates for primary TL, salvage TL, primary TL with pharyngeal reconstruction, or salvage TL with pharyngeal reconstruction groups were 71%, 72%, 73%, and 71%, respectively. TEP‐related complications occurred in 43% of patients, with no difference in complication rates between primary versus salvage TL or primary versus secondary TEP. For those with complications, TEP success rate was 65%.ConclusionThis study showed TEP speech‐outcome success rates lower than what has been historically reported. There was no significant difference in TEP speech outcome between primary versus salvage TL or primary versus secondary TEP. Patients with TEP‐related complications had TEP speech‐outcome success rates comparable to those without any complication. TEP may continue to be a superior option as a mode of speech in patients with TL, including those undergoing salvage TL.Level of Evidence4. Laryngoscope, 124:2508–2512, 2014
A systematic review of the quality of randomized controlled trials in head and neck oncology surgery
Authors: Carlton Daniel A. , Kocherginsky Masha , Langerman Alexander J. 
Published: April 2014

Objectives/HypothesisTo determine the quality of randomized controlled trials (RCTs) in head and neck surgery in which surgery was a primary intervention.Data SourcesPotential articles were identified in PubMed without publication date restrictions.Review MethodsArticles were scored using the CONSORT checklist and the relationship between the checklist score and whether the first and/or last authors were surgeons was investigated. Differences in the checklist score based on how many surgeons were among the first and last authors of the study were analyzed using the Kruskal‐Wallis test. Fisher's exact test was used to examine if there was a significant difference of the reporting of individual items from the checklist between surgeons and nonsurgeons. A nonparametric trend test was used to determine whether there was a difference in the reporting of individual items based on whether there were none, one, or two surgeons among first and last authors.ResultsA total of 38 publications satisfied the inclusion criteria. There was a trend toward lower quality for studies in which surgeons were either first, last, or both first and last authors compared to studies that were first‐authored and last‐authored by nonsurgeons (P = 0.068). Nonsurgeons were more likely to report on critical elements regarding hypothesis, sample size determination, randomization, and eligibility of centers (P = 0.023–0.058).ConclusionThe quality of RCTs in head and neck surgery is poor. Improved training in conducting and reporting clinical research is needed in otolaryngology residencies. Laryngoscope, 125:146–152, 2015
Organization of the Escherichia coli aerobic enzyme complexes of oxidative phosphorylation in dynamic domains within the cytoplasmic membrane
Authors: Erhardt Heiko , Dempwolff Felix , Pfreundschuh Moritz , Riehle Marc , Schäfer Caspar , Pohl Thomas , Graumann Peter , Friedrich Thorsten 
Published: April 2014

AbstractThe Escherichia coli cytoplasmic membrane contains the enzyme complexes of oxidative phosphorylation (OXPHOS). Not much is known about their supramolecular organization and their dynamics within the membrane in this model organism. In mitochondria and other bacteria, it was demonstrated by nondenaturing electrophoretic methods and electron microscopy that the OXPHOS complexes are organized in so‐called supercomplexes, stable assemblies with a defined number of the individual enzyme complexes. To investigate the organization of the E. coli enzyme complexes of aerobic OXPHOS in vivo, we established fluorescent protein fusions of the NADH:ubiquinone oxidoreductase, the succinate:ubiquinone oxidoreductase, the cytochrome bd‐I, and the cytochrome bo3 terminal oxidases, and the FoF1 ATP‐synthase. The fusions were integrated in the chromosome to prevent artifacts caused by protein overproduction. Biochemical analysis revealed that all modified complexes were fully assembled, active, and stable. The distribution of the OXPHOS complexes in living cells was determined using total internal reflection fluorescence microscopy. The dynamics within the membrane were detected by fluorescence recovery after photobleaching. All aerobic OXPHOS complexes showed an uneven distribution in large mobile patches within the E. coli cytoplasmic membrane. It is discussed whether the individual OXPHOS complexes are organized as clustered individual complexes, here called “segrazones.”
Identification of dynapenia in older adults through the use of grip strength t‐scores
Authors: Bohannon Richard W , Magasi Susan 
Published: April 2014

ABSTRACTIntroduction: The aim of this study was to generate reference values and t‐scores (1.0–2.5 standard deviations below average) for grip strength for healthy young adults and to examine the utility of t‐scores from this group for the identification of dynapenia in older adults. Methods: Our investigation was a population‐based, general community secondary analysis of cross‐sectional grip strength data utilizing the NIH Toolbox Assessment norming sample. Participants consisted of community‐dwelling adults, with age ranges of 20–40 years (n = 558) and 60–85 years (n = 390). The main outcome measure was grip strength using a Jamar plus dynamometer. Results: Maximum grip strengths were consistent over the 20–40‐year age group [men 108.0 (SD 22.6) pounds, women 65.8 (SD 14.6) pounds]. Comparison of older group grip strengths to those of the younger reference group revealed (depending on age strata) that 46.2–87.1% of older men and 50.0–82.4% of older women could be designated as dynapenic on the basis of t‐scores. Conclusions: The use of reference value t‐scores from younger adults is a promising method for determining dynapenia in older adults. Muscle Nerve 51: 102–105, 2015
Assessment of the urodynamic diagnosis in patients with urinary incontinence associated with normal pressure hydrocephalus
Authors: Campos‐Juanatey Félix , Gutiérrez‐Baños José Luis , Portillo‐Martín José Antonio , Zubillaga‐Guerrero Sergio 
Published: April 2014

AimsTo assess the urodynamic patterns present in patients with adult normal pressure hydrocephalus (NPH) in our institution.MethodsRetrospectively conducted study on patients diagnosed with NPH by the Neurosurgery Department of our institution, without etiological treatment or urogynecological disorders, who underwent an urodynamic study (UDS) performed according to methods proposed by the International Society of Continence (ICS). Clinical information, complementary tests and UDS were collected, and descriptive analysis was performed, with special focus in urodynamic final diagnosis.ResultsEighty‐one UDS performed between 2003 and 2013. Fifty‐one Males (63%). Mean age: 74.89 ± 8.58 years old (range 52–88 years). Classical triad of symptoms: gait disturbance, dementia, and urinary incontinence (UI) presented in 48.1%. Urinary urgency in 80.9% and UI in 70%. In two cases (2.5%) UDS was not valuable. Urodynamic features of the 79 remaining studies revealed overactive detrusor (OD) in 56 patients (70.9%), being associated with Stress UI (SUI) in one case and with bladder outlet obstruction (BOO) in 19. SUI in six patients (7.6%) and BOO in five (6.3%). Detrusor underactivity in four cases (5%) and normal study in eight (10.1%). About 47.1% of males presented BOO. Cerebrospinal fluid shunt surgery was performed on 32 patients during follow‐up, with subsequent clinical improvement in 90.6% of them.ConclusionsOD was the most frequent diagnosis within UDS conducted on adult NPH patients in our institution, with BOO in an elevated percentage of them. Etiological treatment led to symptomatic improvement in most of patients. Neurourol. Urodynam. 34:465–468, 2015. © 2014 Wiley Periodicals, Inc.
geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees
Authors: Pennell Matthew W. , Eastman Jonathan M. , Slater Graham J. , Brown Joseph W. , Uyeda Josef C. , FitzJohn Richard G. , Alfaro Michael E. , Harmon Luke J. 
Published: April 2014

Abstract
Summary:  Phylogenetic comparative methods are essential for addressing evolutionary hypotheses with interspecific data. The scale and scope of such data have increased dramatically in the past few years. Many existing approaches are either computationally infeasible or inappropriate for data of this size. To address both of these problems, we present geiger v2.0 , a complete overhaul of the popular R package geiger . We have reimplemented existing methods with more efficient algorithms and have developed several new approaches for accomodating heterogeneous models and data types.
Availability and implementation:  This R package is available on the CRAN repository http://cran.r-project.org/web/packages/geiger/ . All source code is also available on github http://github.com/mwpennell/geiger-v2 . geiger v2.0 depends on the ape package.
Contact:   mwpennell@gmail.com
Supplementary information:   Supplementary data are available at Bioinformatics online
methylC Track: visual integration of single-base resolution DNA methylation data on the WashU EpiGenome Browser
Authors: Zhou Xin , Li Daofeng , Lowdon Rebecca F. , Costello Joseph F. , Wang Ting 
Published: April 2014

Abstract
Summary: We present methylC track, an efficient mechanism for visualizing single-base resolution DNA methylation data on a genome browser. The methylC track dynamically integrates the level of methylation, the position and context of the methylated cytosine (i.e. CG, CHG and CHH), strand and confidence level (e.g. read coverage depth in the case of whole-genome bisulfite sequencing data). Investigators can access and integrate these information visually at specific locus or at the genome-wide level on the WashU EpiGenome Browser in the context of other rich epigenomic datasets.
Availability and implementation: The methylC track is part of the WashU EpiGenome Browser, which is open source and freely available at http://epigenomegateway.wustl.edu/browser/ . The most up-to-date instructions and tools for preparing methylC track are available at http://epigenomegateway.wustl.edu/+/cmtk .
Contact: twang@genetics.wustl.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Direct calculation of elementary flux modes satisfying several biological constraints in genome-scale metabolic networks
Authors: Pey Jon , Planes Francisco J. 
Published: April 2014

Abstract
Motivation: The concept of Elementary Flux Mode (EFM) has been widely used for the past 20 years. However, its application to genome-scale metabolic networks (GSMNs) is still under development because of methodological limitations. Therefore, novel approaches are demanded to extend the application of EFMs. A novel family of methods based on optimization is emerging that provides us with a subset of EFMs. Because the calculation of the whole set of EFMs goes beyond our capacity, performing a selective search is a proper strategy.
Results: Here, we present a novel mathematical approach calculating EFMs fulfilling additional linear constraints. We validated our approach based on two metabolic networks in which all the EFMs can be obtained. Finally, we analyzed the performance of our methodology in the GSMN of the yeast Saccharomyces cerevisiae by calculating EFMs producing ethanol with a given minimum carbon yield. Overall, this new approach opens new avenues for the calculation of EFMs in GSMNs.
Availability and implementation: Matlab code is provided in the supplementary online materials
Contact: fplanes@ceit.es .
Supplementary information: Supplementary data are available at Bioinformatics online.
The Biosynthetic Pathway of Indole-3-Carbaldehyde and Indole-3-Carboxylic Acid Derivatives in Arabidopsis
Authors: Böttcher Christoph , Chapman Alexandra , Fellermeier Franziska , Choudhary Manisha , Scheel Dierk , Glawischnig Erich 
Published: April 2014

Abstract
Indolic secondary metabolites play an important role in pathogen defense in cruciferous plants. In Arabidopsis (Arabidopsis thaliana), in addition to the characteristic phytoalexin camalexin, derivatives of indole-3-carbaldehyde (ICHO) and indole-3-carboxylic acid (ICOOH) are synthesized from tryptophan via the intermediates indole-3-acetaldoxime and indole-3-acetonitrile. Based on feeding experiments combined with nontargeted metabolite profiling, their composition in nontreated and silver nitrate (AgNO3)-treated leaf tissue was comprehensively analyzed. As major derivatives, glucose conjugates of 5-hydroxyindole-3-carbaldehyde, ICOOH, and 6-hydroxyindole-3-carboxylic acid were identified. Quantification of ICHO and ICOOH derivative pools after glucosidase treatment revealed that, in response to AgNO3 treatment, their total accumulation level was similar to that of camalexin. ARABIDOPSIS ALDEHYDE OXIDASE1 (AAO1), initially discussed to be involved in the biosynthesis of indole-3-acetic acid, and Cytochrome P450 (CYP) 71B6 were found to be transcriptionally coexpressed with camalexin biosynthetic genes. CYP71B6 was expressed in Saccharomyces cerevisiae and shown to efficiently convert indole-3-acetonitrile into ICHO and ICOOH, thereby releasing cyanide. To evaluate the role of both enzymes in the biosynthesis of ICHO and ICOOH derivatives, knockout and overexpression lines for CYP71B6 and AAO1 were established and analyzed for indolic metabolites. The observed metabolic phenotypes suggest that AAO1 functions in the oxidation of ICHO to ICOOH in both nontreated and AgNO3-treated leaves, whereas CYP71B6 is relevant for ICOOH derivative biosynthesis specifically after induction. In summary, a model for the biosynthesis of ICHO and ICOOH derivatives is presented.
HEAT-INDUCED TAS1 TARGET1Mediates Thermotolerance via HEAT STRESS TRANSCRIPTION FACTOR A1a–Directed Pathways inArabidopsis
Authors: Li Shuxia , Liu Jinxin , Liu Zhongyuan , Li Xiaorong , Wu Feijie , He Yuke 
Published: April 2014

AbstractMany heat stress transcription factors (Hsfs) and heat shock proteins (Hsps) have been identified to play important roles in the heat tolerance of plants. However, many of the key factors mediating the heat response pathways remain unknown. Here, we report that two genes, which are targets of TAS1 (trans-acting siRNA precursor 1)–derived small interfering RNAs that we named HEAT-INDUCED TAS1 TARGET1 (HTT1) and HTT2, are involved in thermotolerance. Microarray analysis revealed that the HTT1 and HTT2 genes were highly upregulated in Arabidopsis thaliana seedlings in response to heat shock. Overexpression of TAS1a, whose trans-acting small interfering RNAs target the HTT genes, elevated accumulation of TAS1-siRNAs and reduced expression levels of the HTT genes, causing weaker thermotolerance. By contrast, overexpression of HTT1 and HTT2 upregulated several Hsf genes, leading to stronger thermotolerance. In heat-tolerant plants overexpressing HsfA1a, the HTT genes were upregulated, especially at high temperatures. Meanwhile, HsfA1a directly activated HTT1 and HTT2 through binding to their promoters. HTT1 interacted with the heat shock proteins Hsp70-14 and Hsp40 and NUCLEAR FACTOR Y, SUBUNIT C2. Taken together, these results suggest that HTT1 mediates thermotolerance pathways because it is targeted by TAS1a, mainly activated by HsfA1a, and acts as cofactor of Hsp70-14 complexes.