bluuebunny/crossref_metadata_2025 huggingface dataset:
The development of a gridded weather typing classification scheme
Authors: Lee Cameron C.
Published: April 2014

Gridded 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/Hypothesis

To 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 Design

Prospective cohort study.

Methods

The 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).

Results

Three 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).

Conclusion

The 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 Evidence

2c. 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/Hypothesis

To describe the speech rehabilitation outcomes of patients undergoing total laryngectomy (TL) in the 21st century.

Study Design

Retrospective chart review.

Setting

Tertiary academic center

Subjects and Methods

Retrospective 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.

Results

Overall 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%.

Conclusion

This 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 Evidence

4. 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/Hypothesis

To determine the quality of randomized controlled trials (RCTs) in head and neck surgery in which surgery was a primary intervention.

Data Sources

Potential articles were identified in PubMed without publication date restrictions.

Review Methods

Articles 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.

Results

A 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).

Conclusion

The 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

The 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

Introduction: 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

Aims

To assess the urodynamic patterns present in patients with adult normal pressure hydrocephalus (NPH) in our institution.

Methods

Retrospectively 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.

Results

Eighty‐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.

Conclusions

OD 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.
Do female and ethnically diverse executives endure inequity in the CEO position or do they benefit from their minority status? An empirical examination
Authors: Hill Aaron D. , Upadhyay Arun D. , Beekun Rafik I.
Published: April 2014

We present competing hypotheses regarding whether gender and ethnic minority CEOs endure inequities resulting in lower compensation and higher likelihood of job exit or benefit from their valuable, rare, and inimitable minority status, resulting in higher compensation and lower likelihood of job exit. Using a longitudinal sample, we find support for the resource‐based hypothesis regarding compensation that suggests CEOs benefit from their minority status to receive higher compensation than white male CEOs receive. However, we also find mixed support for our hypotheses relating CEO minority status to the likelihood of exit. We find that the effects of minority status on likelihood of exit are significantly different for female and ethnic minority CEOs such that the former relationship is negative while the latter is positive. Copyright © 2014 John Wiley & Sons, Ltd.
Mutant p53 exerts oncogenic effects through microRNAs and their target gene networks
Authors: Li Xiao Ling , Jones Matthew F. , Subramanian Murugan , Lal Ashish
Published: April 2014

MicroRNAs are potent regulators of gene expression and modulate multiple cellular processes including proliferation, differentiation and apoptosis. A number of microRNAs have been shown to be regulated by p53, the most frequently mutated gene in human cancer. It is has been demonstrated that some mutant p53 proteins not only lose tumor suppressor activity, but also acquire novel oncogenic functions that are independent of wild‐type p53. In this review, we highlight recent evidences suggesting that some mutant p53 proteins regulate the expression of specific microRNAs to gain oncogenic functions and identify a gene network regulated by the microRNAs downstream of mutant p53.
Digestion proteomics: tracking lactoferrin truncation and peptide release during simulated gastric digestion
Authors: Grosvenor Anita J. , Haigh Brendan J. , Dyer Jolon M.
Published: April 2014

Peptide release profiles from lactoferrin were tracked and characterised during simulated gastric digestion using a novel quantitative proteomic approach.
A highly responsive UV photodetector based on hierarchical TiO2 nanorod/nanoparticle composite
Authors: Zheng Wenji , Li Xiangcun , He Gaohong , Yan Xiaoming , Zhao Rui , Dong Chunxu
Published: April 2014

The large surface area provided by TiO2 nanoparticles, the well-defined electron transport pathway offered by TiO2 nanorods and the homojunction formed at the interface between them contribute to the fast and high photoresponse of a hierarchical composite.
Acetylsalicylic acid (ASA) increases the solubility of cholesterol when incorporated in lipid membranes
Authors: Alsop Richard J. , Barrett Matthew A. , Zheng Songbo , Dies Hannah , Rheinstädter Maikel C.
Published: April 2014

While a high cholesterol concentration of 40 mol% cholesterol leads to the formation of immiscible cholesterol bilayers in saturated lipid membranes, the addition of ASA was found to significantly increase the fluidity of the bilayers and to dissolve the cholesterol plaques.
Land Markets and the Value of Water: Hedonic Analysis Using Repeat Sales of Farmland
Authors: Buck Steven , Auffhammer Maximilian , Sunding David
Published: April 2014

The lack of robust water markets makes it difficult to value irrigation water. Because water rights are appurtenant to land, it is possible to infer the value of water from observed differences in the market price of land. We use panel data on repeat farmland sales in California's San Joaquin Valley to estimate a hedonic regression equation with parcel fixed effects. This controls for sources of omitted variables bias and allows us to recover the value of irrigation water to landowners in our sample. We show that a more traditional cross‐sectional regression results in an artificially low value of irrigation water.
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

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

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

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.
Whole Genome Bisulfite Sequencing of Cell Free DNA and its Cellular Contributors Uncovers Placenta Hypomethylated Domains
Authors: Jensen Taylor , Kim Sung K , Zhu Zhanyang , Chin Christine , Gebhard Claudia , Lu Tim , Deciu Cosmin , van den Boom Dirk , Ehrich Mathias
Published: April 2014

Background Circulating cell free fetal DNA has enabled non-invasive prenatal fetal aneuploidy testing without direct discrimination of the genetically distinct maternal and fetal DNA. Current testing may be improved by specifically enriching the sample material for fetal DNA. DNA methylation may allow for such a separation of DNA and thus support additional clinical opportunities; however, this depends on knowledge of the methylomes of ccf DNA and its cellular contributors. Results Whole genome bisulfite sequencing was performed on a set of unmatched samples including ccf DNA from 8 non-pregnant (NP) and 7 pregnant female donors and genomic DNA from 7 maternal buffy coat and 5 placenta samples. We found CpG cytosines within longer fragments were more likely to be methylated, linking DNA methylation and fragment size in ccf DNA. Comparison of the methylomes of placenta and NP ccf DNA revealed many of the 51,259 identified differentially methylated regions (DMRs) were located in domains exhibiting consistent placenta hypomethylation across millions of consecutive bases, regions we termed placenta hypomethylated domains (PHDs). We found PHDs were consistently located within regions exhibiting low CpG and gene density. DMRs identified when comparing placenta to NP ccf DNA were recapitulated in pregnant ccf DNA, confirming the ability to detect differential methylation in ccf DNA mixtures. Conclusions We generated methylome maps for four sample types at single base resolution, identified a link between DNA methylation and fragment length in ccf DNA, identified DMRs between sample groups, and uncovered the presence of megabase-size placenta hypomethylated domains. Furthermore, we anticipate these results to provide a foundation to which future studies using discriminatory DNA methylation may be compared.
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

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

Many 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.
Translation and validation of the Turkish language version of the Rheumatoid Arthritis Disease Activity Index‐5
Authors: Sunar Ismihan , Yilmaz Tasdelen Ozlem , Garip Cimen Yesim , Bodur Hatice
Published: April 2014

Aim

The purpose of this study was to translate the Rheumatoid Arthritis Disease Activity Index‐5 (RADAI‐5), which is a tool for measuring disease activity in rheumatoid arthritis (RA) patients, into Turkish language and prove its validity, reliability and sensitivity to changes.

Methods

Translation from the original German version was performed according to the standardized methods. One hundred and two patients with RA completed in the Turkish RADAI‐5 twice within 3 days interval. Internal consistency and test–retest reliability was investigated by calculating Cronbach's alpha and intra‐class correlation coefficients (ICC), respectively. Validity was assessed by analyzing the correlations between the Turkish RADAI‐5 and some measurement tools evaluating the disease activity, functional status and quality of life. To test the scale's responsiveness to the changes, another 23 patients with uncontrolled disease activity and three newly diagnosed RA patients completed the RADAI‐5 before and after a biologic agent or methotrexate treatment.

Results

There were no floor or ceiling effects. Cronbach's alpha (0.91) and ICC (0.997) values certified the Turkish version's reliability. Strong correlations between the Turkish questionnaire and Disease Activity Score‐28 (DAS28), DAS28‐CRP, DAS28‐three variables, Health Assessment Questionnaire, Rheumatoid Arthritis Quality of Life questionnaire, patient's and doctor's global assessments, tender joint count proved the convergent validity of the scale. Effect size (3.08) demonstrated that the Turkish RADAI‐5 is sensitive to the changes.

Conclusion

The Turkish RADAI‐5 is a feasible, reliable and valid questionnaire and sensitive to changes; thus it can be used to monitor disease activity in Turkish RA patients.
Tuberculosis risk and anti‐tumour necrosis factor agents in rheumatoid arthritis: a critical appraisal of national registry data
Authors: Scrivo Rossana , Armignacco Orlando
Published: April 2014

Tuberculosis (TB) remains a major global health problem. In patients with rheumatoid arthritis (RA), the risk of reactivation of latent TB infection (LTBI) is increased and treatment with tumour necrosis factor (TNF) antagonists further increases this risk. However, interpretation of results describing comparative TB risk during therapy with different TNF antagonists is difficult. This is not only a result of different patient ethnic groups and background TB rates, but also because of differing methods of data acquisition. This paper offers a critical appraisal of registry data pertaining to RA patients treated with different anti‐TNF agents, focusing on methodological approaches that may limit the generalizability of findings or invalidate the direct comparison of TB risk between different national registries. Underlying factors that can make data interpretation challenging are discussed, including differences in methods for TB diagnosis or data collection and reporting, as well as background TB risk. The introduction of special monitoring systems, such as prospective multinational registries, to strengthen surveillance and better quantify the extent of under‐reporting is required, especially in countries where the background TB risk is high.
A systematic review of the clinical relevance of repetitive transcranial magnetic stimulation
Authors: Lepping P. , Schönfeldt‐Lecuona C. , Sambhi R. S. , Lanka S. V. N. , Lane S. , Whittington R. , Leucht S. , Poole R.
Published: April 2014

Objective

Repetitive transcranial magnetic stimulation (rTMS) is an approved treatment for depression. The clinical relevance of its efficacy is unclear. The clinical relevance of findings in the rTMS literature was assessed by translating Hamilton Depression Rating Scale (HAMD) data into Clinical Global Impression–Improvement scale (CGI‐I) scores.

Method

We performed electronic searches of MEDLINE, Embase, PsycINFO, PubMed and Cochrane Central Register of Controlled Trials for RCTs and non‐RCT trials on rTMS using Hamilton Depression Rating Scale (HAMD). Articles were included if published in English before January 2014. We translated HAMD scores into nominal CGI‐I scores for rTMS for depression and for treatment‐resistant depression (TRD).

Results

About 960 abstracts were retrieved. Sixty‐three studies were included, yielding 130 study arms. For depression, the mean percentage change in HAMD scores in all sham‐controlled rTMS treatment arms was 35.63 (SD 16.35) and for sham‐rTMS 23.33 (SD 16.51). For TRD, active rTMS in sham‐controlled studies showed a mean HAMD percentage reduction of 45.21 (SD 10.94) versus 25.04 (SD 17.55) for sham‐rTMS. When aggregated scores were translated into notional CGI‐I scores, for the treatment of depression, the notional CGI‐I score difference between rTMS and sham‐rTMS was 0.5 in favour of rTMS; for TRD, it was 0.75 in favour of rTMS. Differences between rTMS and sham‐rTMS were bigger when all study arms were combined.

Conclusion

Whilst rTMS appears to be efficacious for both non‐refractory and treatment‐resistant depression, the clinical relevance of its efficacy is doubtful.
Evaluating national guidelines for the prophylactic treatment of respiratory syncytial virus in children with congenital heart disease
Authors: Granbom Elin , Fernlund Eva , Sunnegårdh Jan , Lundell Bo , Naumburg Estelle
Published: April 2014

Aim

This is the first study to evaluate compliance with the 2003 Swedish national guidelines for prophylactic treatment of respiratory syncytial virus (RSV) in children with congenital heart disease (CHD). We estimated the relative risk (RR) of children with CHD being hospitalised with a RSV infection, studied the extent to which RSV prophylactic treatment with palivizumab corresponded to the guidelines and determined the morbidity of children with CHD who developed RSV infection despite prophylaxis.

Methods

This national observational study comprised prospectively registered data on 219 children with CHD treated with palivizumab, medical records on RSV cases and information on hospitalisation rates of children with CHD and RSV infection.

Results

The calculated RR of children with CHD being hospitalised with RSV infection was 2.06 (95% CI 1.6–2.6; p < 0.0001) compared with children without CHD. Approximately half of the patients (49%) born before the RSV season and 25% born during the RSV season did not start treatment as recommended by the guidelines.

Conclusion

Having CHD increased the rate and estimated RR of children being hospitalised with RSV infection. The guidelines were not followed for about half of the children born before a RSV season and a quarter of the children born during a RSV season and need updating.
Multiobjective Optimization on Antiplatelet Effects of Three Components Combination by Quantitative Composition–activity Relationship Modeling and Weighted‐Sum Method
Authors: Huang Yi , Jiang Wei , Xiao Yang , Wang Yi , Wang Yi
Published: April 2014

Multicomponent therapeutic has become an increasingly favored strategy for treating complex diseases in recent years. In this study, a multiple objective optimization approach was proposed to design the optimal combination of three components for antiplatelet activity. The platelet aggregation assays induced by three different ways, adenosine diphosphate, arachidonic acid, and collagen, were applied to evaluate the in vitro antiplatelet activities of three active components derived from a traditional Chinese medicine. After analyzing this dataset by quantitative composition–activity relationship modeling, a weighted‐sum optimization method was adopted to calculate the optimal ratio between three components for antiplatelet effects. Further experiments validated our method and showed that better antiplatelet activity was exerted by the optimized combination than the individual component or other combinations. Our findings suggested that the proposed multiobjective optimization approach is a novel method for multicomponent drug design.
Hypertrophic pyloric stenosis in twins; genetic or environmental factors
Authors: Gezer H.Ö. , Oguzkurt P. , Temiz A. , Hicsonmez A.
Published: April 2014

The etiology of infantile hypertrophic pyloric stenosis (IHPS) remains obscure. Over 120 years after the condition has become a clinical entity the debate whether the cause of IHPS is genetic, environmental or both, has not yet reached a final conclusion. Herein, we present a pair of monozygotic male twins with IHPS together with a review of the literature. We aimed to support genetic pre‐disposition in the epidemiology of IHPS, adding a twin data to the literature and to review the associated articles about the pathogenesis and inheritance patterns.
Phenotypic heterogeneity and mutational spectrum in a cohort of 45 Italian males subjects with X‐linked ectodermal dysplasia
Authors: Guazzarotti L. , Tadini G. , Mancini G.E. , Giglio S. , Willoughby C.E. , Callea M. , Sani I. , Nannini P. , Mameli C. , Tenconi A.A. , Mauri S. , Bottero A. , Caimi A. , Morelli M. , Zuccotti G.V.
Published: April 2014

Ectodermal dysplasias (EDs) are a group of genetic disorders characterized by the abnormal development of the ectodermal‐derived structures. X‐linked hypohidrotic ectodermal dysplasia, resulting from mutations in ED1 gene, is the most common form. The main purpose of this study was to characterize the phenotype spectrum in 45 males harboring ED1 mutations. The study showed that in addition to the involvement of the major ectodermal tissues, the majority of patients also have alterations of several minor ectodermal‐derived structures. Characterizing the clinical spectrum resulting from ED1 gene mutations improves diagnosis and can direct clinical care.
Contribution of copy number variations in CMT1X: a retrospective study
Authors: Capponi S. , Geroldi A. , Pezzini I. , Gulli R. , Ciotti P. , Ursino G. , Lamp M. , Reni L. , Schenone A. , Grandis M. , Mandich P. , Bellone E.
Published: April 2014

Background and purpose

Charcot−Marie−Tooth disease type 1X (CMT1X) is an X‐linked dominant hereditary motor‐sensory peripheral neuropathy, which results from mutations in the Gap Junction B1 (GJB1) gene. In a few cases, gene deletions have been linked to the disease, but their relative contribution in the pathogenesis of CMT1X has not been assessed yet. Herein a retrospective study to establish the incidence of gene deletions is described.

Methods

Copy number variation analysis was performed by multiplex ligation‐dependent probe amplification, whilst the breakpoints were defined by Sanger sequencing.

Results

A novel GJB1 deletion was identified in a family presenting with a classical CMT1X phenotype. The rearrangement includes the coding and the regulatory regions of GJB1.

Conclusions

GJB1 deletions appear to be a rare but not insignificant cause of CMT1X and are associated with a typical disease phenotype. Accordingly, patients negative for point mutations whose pedigree and clinical records strongly suggest the possibility of CMT1X should be tested for GJB1 copy number variations.
Climate change and geothermal ecosystems: natural laboratories, sentinel systems, and future refugia
Authors: O'Gorman Eoin J. , Benstead Jonathan P. , Cross Wyatt F. , Friberg Nikolai , Hood James M. , Johnson Philip W. , Sigurdsson Bjarni D. , Woodward Guy
Published: April 2014

Understanding and predicting how global warming affects the structure and functioning of natural ecosystems is a key challenge of the 21st century. Isolated laboratory and field experiments testing global change hypotheses have been criticized for being too small‐scale and overly simplistic, whereas surveys are inferential and often confound temperature with other drivers. Research that utilizes natural thermal gradients offers a more promising approach and geothermal ecosystems in particular, which span a range of temperatures within a single biogeographic area, allow us to take the laboratory into nature rather than vice versa. By isolating temperature from other drivers, its ecological effects can be quantified without any loss of realism, and transient and equilibrial responses can be measured in the same system across scales that are not feasible using other empirical methods. Embedding manipulative experiments within geothermal gradients is an especially powerful approach, informing us to what extent small‐scale experiments can predict the future behaviour of real ecosystems. Geothermal areas also act as sentinel systems by tracking responses of ecological networks to warming and helping to maintain ecosystem functioning in a changing landscape by providing sources of organisms that are preadapted to different climatic conditions. Here, we highlight the emerging use of geothermal systems in climate change research, identify novel research avenues, and assess their roles for catalysing our understanding of ecological and evolutionary responses to global warming.
A simplified method for monomeric carbohydrate analysis of corn stover biomass
Authors: Mourtzinis Spyridon , Arriaga Francisco J. , Bransby David , Balkcom Kipling S.
Published: April 2014

Constituent determination of biomass for theoretical ethanol yield (TEY) estimation requires the removal of nonstructural carbohydrates prior to analysis to prevent interference with the analytical procedure. According to the accepted US Department of Energy‐National Renewable Energy Laboratory (NREL) method, biomass extractives in corn stover should be removed by a two‐step extraction process. Alternatively, Neutral Detergent Fiber method (NDF) is a fast and cost‐effective method used to determine structural carbohydrates of forage biomass. The objective of this study was to determine whether the NDF method can be used as an alternative to the NREL extraction procedure for corn (Zea mays L.) stover biomass. Arabinan content varied between the two methods. However, glucan, xylan, and TEYs were not statistically different. Furthermore, the average TEYs per unit of mass and unit of area varied by 2.0 and 1.9%, respectively. Additionally, the NDF extraction procedure was faster and less expensive than the NREL procedure.
Shelf life stability of red‐fleshed plum nectars: role of polyphenol fortification on quality parameters
Authors: de Beer Dalene , Joubert Elizabeth , Steyn Naomi , Muller Magdalena
Published: April 2014

The effect of polyphenol fortification of red‐fleshed plum nectars by addition of plum skin extract on the stability of quality, defined in terms of sensory attributes, phenolic composition and antioxidant activity, during shelf life storage was investigated. The sensory attributes were stable throughout the 3‐month storage period at 5 °C for the control and fortified formulations. Among the phenolic compounds measured only the anthocyanins decreased during the storage period; however, the total antioxidant activity was not affected. The loss of red colour was less pronounced compared to the loss of anthocyanins for both formulations. This might be attributed to enhanced co‐pigmentation as the content of the co‐pigment, neochlorogenic acid, increased, while flavonols remained stable during storage. Polyphenol fortification enhanced the retention of red colour, polyphenol content and total antioxidant capacity compared to the control formulation.
Effect of Dorsal Acetabular Rim Loss on Stability of the Zurich Cementless Total Hip Acetabular Cup in Dogs
Authors: DeSandre‐Robinson Dana M. , Kim Stanley E. , Peck Jeffrey N. , Coggeshall Jason D. , Tremolada Giovanni , Pozzi Antonio
Published: April 2014

Objective

To evaluate magnitude and mode of acute load to failure of the Zurich Cementless acetabular cup prosthesis in cadaveric specimens with and without 50% dorsal acetabular rim loss.

Study Design

In vitro mechanical study.

Sample Population

Cadaveric hemipelves of adult dogs (n = 8).

Methods

Each pair of hemipelves was prepared by dissection of surrounding musculature and implantation of a Zurich Cementless acetabular cup prosthesis. One hemipelvis had the dorsal rim left intact (group 1) and the contralateral hemipelvis had 50% of the dorsal rim excised (group 2). Each hemipelvis underwent acute load to failure with an axial load applied through a prosthetic femoral head. Load at failure was compared between hemipelves with and without dorsal rim loss with a paired t‐test; P < .05 was considered significant.

Results

Mean failure load was not significantly different between group 1 (3,713 ± 362 N) and group 2 (3,640 ± 751 N; P = .8). Bone fracture (n = 6), ventroversion of the cup (1), and absolute failure unreached at 6,000 N (1) occurred in group 1 and bone fracture (6), ventroversion of cup (1), and cup loosening (1) occurred in group 2.

Conclusions

Zurich Cementless acetabular cup stability does not appear to be compromised by 50% acetabular rim loss at normal physiologic weight bearing loads. Thus, for this system, modifying procedures such as augmentation of the dorsal acetabular rim or deeper reaming for acetabular bed preparation may not be necessary with up to 50% dorsal rim loss with the Zurich Cementless acetabular cup.
Male mate choice relies on major histocompatibility complex class I in a sex‐role‐reversed pipefish
Authors: Roth O. , Sundin J. , Berglund A. , Rosenqvist G. , Wegner K. M.
Published: April 2014

Mate choice for compatible genes is often based on genes of the major histocompatibility complex (MHC). AlthoughMHC‐based mate choice is commonly observed in female choice, male mate choice remains elusive. In particular, if males have intense paternal care and are thus the choosing sex, male choice for females with dissimilarMHCcan be expected. Here, we investigated whether male mate choice relies onMHCclass I genes in the sex‐role reversed pipefishSyngnathus typhle. In a mate choice experiment, we determined the relative importance of visual and olfactory cues by manipulating visibility and olfaction. We found that pipefish males chose females that maximize sequence‐based amino acid distance betweenMHCclass I genotypes in the offspring when olfactory cues were present. Under visual cues, large females were chosen, but in the absence of visual cues, the choice pattern was reversed. The use of sex‐role reversed species thus revealed that sexual selection can lead to the evolution of male mate choice forMHCclass I genes.
Recognizing odd smells and ejection of brood parasitic eggs. An experimental test in magpies of a novel defensive trait against brood parasitism
Authors: Soler J. J. , Pérez‐Contreras T. , De Neve L. , Macías‐Sánchez E. , Møller A. P. , Soler M.
Published: April 2014

One of the most important defensive host traits against brood parasitism is the detection and ejection of parasitic eggs from their nests. Here, we explore the possible role of olfaction in this defensive behaviour. We performed egg‐recognition tests in magpie Pica pica nests with model eggs resembling those of parasitic great spotted cuckoos Clamator glandarius. In one of the experiment, experimental model eggs were exposed to strong or moderate smell of tobacco smoke, whereas those of a third group (control) were cleaned with disinfecting wipes and kept in boxes containing odourless cotton. Results showed that model eggs with strong tobacco scent were more frequently ejected compared with control ones. In another experiment, models were smeared with scents from cloacal wash from magpies (control), cloacal wash or uropygial secretions from cuckoos, or human scents. This experiment resulted in a statistically significant effect of treatment in unparasitized magpie nests in which control model eggs handled by humans were more often rejected. These results provide the first evidence that hosts of brood parasites use their olfactory ability to detect and eject foreign eggs from their nests. These findings may have important consequences for handling procedures of experimental eggs used in egg‐recognition tests, in addition to our understanding of interactions between brood parasites and their hosts.