bluuebunny/crossref_metadata_2025_split huggingface dataset:
The relationship between oxidative stress and autoimmunity in Hashimoto's thyroiditis
Authors: Ates Ihsan , Yilmaz Fatma Meric , Altay Mustafa , Yilmaz Nisbet , Berker Dilek , Güler Serdar 
Published: September 2015

ObjectiveWe have aimed to study the relation between Hashimoto's thyroiditis (HT) and thyroid autoantibodies and oxidative stress parameters in euthyroid, subclinical and overt hypothyroid stages.Design and methodsA total of 124 patients were included in the study; 93 of whom were newly diagnosed with HT (31 patients in each of the euthyroid, subclinical hypothyroid and overt hypothyroid subgroups), aged over 18 and had not received any prior treatment and 31 of whom were healthy volunteers.ResultsTotal oxidant status (TOS) and oxidative stress index (OSI) levels were higher, and total antioxidant status (TAS) and total thiol and arylesterase levels were lower in the overt hypothyroid group compared to other groups. TOS and OSI levels increased, and TAS levels decreased significantly in each phase from euthyroid, subclinical hypothyroid, to overt hypothyroid subgroups among HT patients. There was a negative correlation between TAS, log (paraoxonase1) and paraoxonase1/HDL and anti-thyroid peroxidase and a negative correlation between anti-thyroglobulin and total thiol. It was also determined that overt hypothroidism was an individual predictor that effects all of the oxidative stress parameters, but not total thiol, levels.ConclusionOur results suggest that oxidative stress increases continuously during the development of subclinical hypothyroidism and overt hypothyroidism in patients with HT. To determine whether this is a cause or result, randomized, controlled trials that study the effect of antioxidant treatment on the development of overt hypothyroidism and its consequences, e.g., increase in total cholesterol levels, may be performed in euthyroid and/or subclinical hypothyroid patients with HT.
Disruption of Endocytosis with the Dynamin Mutantshibirets1Suppresses Seizures inDrosophila
Authors: Kroll Jason R , Wong Karen G , Siddiqui Faria M , Tanouye Mark A 
Published: September 2015

AbstractOne challenge in modern medicine is to control epilepsies that do not respond to currently available medications. Since seizures consist of coordinated and high-frequency neural activity, our goal was to disrupt neurotransmission with a synaptic transmission mutant and evaluate its ability to suppress seizures. We found that the mutant shibire, encoding dynamin, suppresses seizure-like activity in multiple seizure–sensitive Drosophila genotypes, one of which resembles human intractable epilepsy in several aspects. Because of the requirement of dynamin in endocytosis, increased temperature in the shits1 mutant causes impairment of synaptic vesicle recycling and is associated with suppression of the seizure-like activity. Additionally, we identified the giant fiber neuron as critical in the seizure circuit and sufficient to suppress seizures. Overall, our results implicate mutant dynamin as an effective seizure suppressor, suggesting that targeting or limiting the availability of synaptic vesicles could be an effective and general method of controlling epilepsy disorders.
Nonlinear analysis of stability for imperfect eccentrically stiffened FGM plates under mechanical and thermal loads based on FSDT. Part 1: Governing equations establishment
Authors: Dung Dao Van , Nga Nguyen Thi 
Published: September 2015

In this paper, the buckling and post-buckling behaviors of eccentrically stiffened functionally graded material (ES-FGM) plates on elastic foundations subjected to in-plane compressive loads or thermal loads are investigated by an analytical solution. The novelty of this work is that FGM plates are reinforced by FGM stiffeners and the temperature, stiffener, foundation are considered. The first-order shear deformation plate theory is used. The thermal elements of plate and stiffeners in fundamental equations are introduced. Theoretical formulations based on the smeared stiffeners technique and the first-order shear deformation plate theory, are derived. The analytical expressions to determine the static critical buckling load and post-buckling load-deflection curves are obtained.
Predicting Ovarian Activity in Women Affected by Early Breast Cancer: A Meta-Analysis-Based Nomogram
Authors: Barnabei Agnese , Strigari Lidia , Marchetti Paolo , Sini Valentina , De Vecchis Liana , Corsello Salvatore Maria , Torino Francesco 
Published: September 2015

Abstract

Background.
The assessment of ovarian reserve in premenopausal women requiring anticancer gonadotoxic therapy can help clinicians address some challenging issues, including the probability of future pregnancies after the end of treatment. Anti-Müllerian hormone (AMH) and age can reliably estimate ovarian reserve. A limited number of studies have evaluated AMH and age as predictors of residual ovarian reserve following cytotoxic chemotherapy in breast cancer patients.

Materials and Methods.
To conduct a meta-analysis of published data on this topic, we searched the medical literature using the key MeSH terms “amenorrhea/chemically induced,” “ovarian reserve,” “anti-Mullerian hormone/blood,” and “breast neoplasms/drug therapy.” Preferred Reporting Items for Systematic Reviews and Meta-Analyses statements guided the search strategy. U.K. National Health Service guidelines were used in abstracting data and assessing data quality and validity. Area under the receiver operating characteristic curve (ROC/AUC) analysis was used to evaluate the predictive utility of baseline AMH and age model.

Results.
The meta-analysis of data pooled from the selected studies showed that both age and serum AMH are reliable predictors of post-treatment ovarian activity in breast cancer patients. Importantly, ROC/AUC analysis indicated AMH was a more reliable predictor of post-treatment ovarian activity in patients aged younger than 40 years (0.753; 95% confidence interval [CI]: 0.602–0.904) compared with those older than 40 years (0.678; 95% CI: 0.491–0.866). We generated a nomogram describing the correlations among age, pretreatment AMH serum levels, and ovarian activity at 1 year from the end of chemotherapy.

Conclusion.
After the ongoing validation process, the proposed nomogram may help clinicians discern premenopausal women requiring cytotoxic chemotherapy who should be considered high priority for fertility preservation counseling and procedures.

Implications for Practice:
In general, a nomogram helps clinicians better visualize a specific risk for a single patient. In premenopausal women affected by early breast cancer who need adjuvant cytotoxic regimens, the proposed nomogram—based on the assessment of pretreatment age and anti-Müllerian hormone serum levels—can assess the personal probability of maintaining ovarian activity at 1 year from the end of chemotherapy. The ongoing validation process is also evaluating other key factors contributing to post-treatment ovarian activity (i.e., type of cytotoxic regimen) and will confirm the nomogram's reliability and clinical utility.
The use of patch testing for the diagnosis of contact dermatitis: an Albanian experience
Authors: Fida Monika , Topi Geriolda , Qirko Etleva , Kellici Suela , Shehu Erjona , Dervishi Orjana , Vasili Ermira 
Published: September 2015

Introduction: The daily increase of using chemical, aromatic and cosmetic products has been associated with significant increase in frequency of skin diseases such as eczemas and contact dermatitis (CD). The aim of this study was to evaluate the use of patch testing (PT) for the diagnosis of CD and provide current data on the frequency of sensitization to various contact allergens among patients with CD in the Albanian population.Methods: We retrospectively analyzed all consecutive patients clinically suspected for CD during the period February 2010 – February 2011, in the outpatient setting. PT was done using Baseline European Series consisting of 31 allergens. Risk factors (age, gender, occupation and place of residence) and sensitization to various contact allergens were evaluated. Results: In total, 193 patients clinically suspected for CD were included in the study and underwent PT. The highest prevalence of CD was found in the age-group of 31-40 years (32.6%), with a statistically significant difference between other age-groups (X2 = 141.2, p<0.01). Positive PT results with at least one allergen were seen in 144 (74.6 %) patients suspected for CD. The two most common allergens were nickel and potassium dichromate. Construction worker and hairdresser were the most affected professions. Females had a chance of 1.8 times higher for having a positive patch test result compare to males (OR = 1.8; 95% CI 0.91 – 3.39).Conclusion: Determination of allergens that cause contact dermatitis is a necessity not only to confirm the correct diagnosis, but also for the qualitative treatment and prevention of the disease. Patch testing, even though an old method, still remain a valuable and non-invasive approach to determine the causes of contact dermatitis.
Laboratory Evaluation of Sorptive Filtration Media Mixtures for Targeted Pollutant Removals from Simulated Stormwater
Authors: Prabhukumar Giridhar , Bhupal Gurmanpreet Singh , Pagilla Krishna R. 
Published: September 2015

ABSTRACT: Urban stormwater pollutants including nutrients, trace metals, polycyclic aromatic hydrocarbons (PAHs), total suspended solids (TSS) and indicator microorganisms (E. coli) were the target pollutants in this study. Their simultaneous removal from synthetic stormwater using different sorptive media was investigated through laboratory‐scale column experiments. The media considered for testing were calcite (C), sand (S), zeolite (Z) and iron filings (Fe0). These media are easily/commercially available, environmentally benign, long lasting (non‐biodegradable), highly permeable and effective in removing multiple target pollutants. Based on individual media testing, three different mixed media compositions were selected (1) C‐Z‐S, (2) C‐S‐Fe0 and (3) C‐Z‐S‐Fe0, for simultaneous removal of target pollutants using column experiments. The mixed media composition, C‐Z‐S‐Fe0 showed significantly better simultaneous removal of all the target pollutants as compared to the other two compositions. These compositions can be tailored to meet site‐specific stormwater pollutant removal in a passive in‐ground sorptive media filter.
Characterization of Stormwater Runoff from a Light Rail Transit Area
Authors: Sajjad Raja Umer , Kim Kyoung Jin , Memon Sheeraz , Sukhbaatar Chinzorig , Paule Ma. Cristina , Lee Bum‐Yeon , Lee Chang‐Hee 
Published: September 2015

ABSTRACT: The monitoring of stormwater runoff from Light Rail Transit (LRT) facilities is insufficient in many regions around the world. In this study, runoff quality and quantity were monitored during operational and non‐operational LRT phases during 2010‐2013. The event mean concentration (EMC) of pollutants showed little statistical variability during both phases. The antecedent dry day (ADD) showed a strong to moderate positive correlation with most pollutant EMCs during the non‐operational phase. The existence and magnitude of the first flush from LRT runoff was found to be similar to those from other transportation land uses. The comparison of LRT runoff data with an adjacent road bridge site showed that the pollutant EMC and unit load were 2 to 9 times higher from the road bridge. It was suggested that LRT automated operation and the elevated track makes this transportation mode a viable option for the management of non‐point source pollution.
The Use of Glyburide Compared With Other Sulfonylureas and the Risk of Cancer in Patients With Type 2 Diabetes
Authors: Tuccori Marco , Wu Jennifer W. , Yin Hui , Majdan Agnieszka , Azoulay Laurent 
Published: September 2015

OBJECTIVETo determine whether the use of glyburide is associated with an increased risk of cancer compared with the use of other second-generation sulfonylureas among patients with type 2 diabetes.RESEARCH DESIGN AND METHODSThe U.K. Clinical Practice Research Datalink was used to conduct a cohort study among 52,600 patients newly prescribed glyburide or other second-generation sulfonylureas between 1 January 1988 and 31 July 2013. A time-dependent Cox proportional hazards model was used to estimate adjusted hazard ratios (HRs) and 95% CIs of any cancer associated with the use of glyburide compared with the use of second-generation sulfonylureas. Secondary analyses were conducted to determine whether the association varied with cumulative duration of use and cumulative dose (expressed as defined daily dose [DDD]).RESULTSDuring 280,288 person-years of follow-up, 4,105 patients were given a new diagnosis of cancer (incidence rate 14.6 per 1,000 person-years). Overall, when compared with the use of other second-generation sulfonylureas, the use of glyburide was associated with a nonsignificant increased risk of any cancer (HR 1.09 [95% CI 0.98–1.22]). In secondary analyses, duration- and dose-response relationships were observed, with longer cumulative durations and cumulative doses associated with an increased risk of any cancer (&gt;36 months: HR 1.21 [95% CI: 1.03–1.42]; &gt;1,096 DDDs: HR 1.27 [95% CI 1.06–1.51]).CONCLUSIONSIn this population-based cohort study, longer cumulative durations and higher cumulative doses of glyburide were associated with an increased risk of cancer.
Aspirin-Exacerbated Respiratory Disease Involves a Cysteinyl Leukotriene–Driven IL-33–Mediated Mast Cell Activation Pathway
Authors: Liu Tao , Kanaoka Yoshihide , Barrett Nora A. , Feng Chunli , Garofalo Denise , Lai Juying , Buchheit Kathleen , Bhattacharya Neil , Laidlaw Tanya M. , Katz Howard R. , Boyce Joshua A. 
Published: September 2015

Abstract
Aspirin-exacerbated respiratory disease (AERD), a severe eosinophilic inflammatory disorder of the airways, involves overproduction of cysteinyl leukotrienes (cysLTs), activation of airway mast cells (MCs), and bronchoconstriction in response to nonselective cyclooxygenase inhibitors that deplete homeostatic PGE2. The mechanistic basis for MC activation in this disorder is unknown. We now demonstrate that patients with AERD have markedly increased epithelial expression of the alarmin-like cytokine IL-33 in nasal polyps, as compared with polyps from aspirin-tolerant control subjects. The murine model of AERD, generated by dust mite priming of mice lacking microsomal PGE2 synthase (ptges−/− mice), shows a similar upregulation of IL-33 protein in the airway epithelium, along with marked eosinophilic bronchovascular inflammation. Deletion of leukotriene C4 synthase, the terminal enzyme needed to generate cysLTs, eliminates the increased IL-33 content of the ptges−/− lungs and sharply reduces pulmonary eosinophilia and basal secretion of MC products. Challenges of dust mite–primed ptges−/− mice with lysine aspirin induce IL-33–dependent MC activation and bronchoconstriction. Thus, IL-33 is a component of a cysLT-driven innate type 2 immune response that drives pathogenic MC activation and contributes substantially to AERD pathogenesis.
Endotoxemia Induces IκBβ/NF-κB–Dependent Endothelin-1 Expression in Hepatic Macrophages
Authors: McKenna Sarah , Gossling Megan , Bugarini Alejandro , Hill Elizabeth , Anderson Aimee L. , Rancourt Raymond C. , Balasubramaniyan Natarajan , El Kasmi Karim C. , Wright Clyde J. 
Published: September 2015

AbstractElevated serum concentrations of the vasoactive protein endothelin-1 (ET-1) occur in the setting of systemic inflammatory response syndrome and contribute to distal organ hypoperfusion and pulmonary hypertension. Thus, understanding the cellular source and transcriptional regulation of systemic inflammatory stress-induced ET-1 expression may reveal therapeutic targets. Using a murine model of LPS-induced septic shock, we demonstrate that the hepatic macrophage is the primary source of elevated circulating ET-1, rather than the endothelium as previously proposed. Using pharmacologic inhibitors, ET-1 promoter luciferase assays, and by silencing and overexpressing NF-κB inhibitory protein IκB expression, we demonstrate that LPS-induced ET-1 expression occurs via an NF-κB–dependent pathway. Finally, the specific role of the cRel/p65 inhibitory protein IκBβ was evaluated. Although cytoplasmic IκBβ inhibits activity of cRel-containing NF-κB dimers, nuclear IκBβ stabilizes NF-κB/DNA binding and enhances gene expression. Using targeted pharmacologic therapies to specifically prevent IκBβ/NF-κB signaling, as well as mice genetically modified to overexpress IκBβ, we show that nuclear IκBβ is both necessary and sufficient to drive LPS-induced ET-1 expression. Together, these results mechanistically link the innate immune response mediated by IκBβ/NF-κB to ET-1 expression and potentially reveal therapeutic targets for patients with Gram-negative septic shock.
Biased Immunoglobulin Light Chain Gene Usage in the Shark
Authors: Iacoangeli Anna , Lui Anita , Naik Ushma , Ohta Yuko , Flajnik Martin , Hsu Ellen 
Published: September 2015

Abstract
This study of a large family of κ L chain clusters in nurse shark completes the characterization of its classical Ig gene content (two H chain isotypes, μ and ω, and four L chain isotypes, κ, λ, σ, and σ-2). The shark κ clusters are minigenes consisting of a simple VL-JL-CL array, where V to J recombination occurs over an ∼500-bp interval, and functional clusters are widely separated by at least 100 kb. Six out of ∼39 κ clusters are prerearranged in the germline (germline joined). Unlike the complex gene organization and multistep assembly process of Ig in mammals, each shark Ig rearrangement, somatic or in the germline, appears to be an independent event localized to the minigene. This study examined the expression of functional, nonproductive, and sterile transcripts of the κ clusters compared with the other three L chain isotypes. κ cluster usage was investigated in young sharks, and a skewed pattern of split gene expression was observed, one similar in functional and nonproductive rearrangements. These results show that the individual activation of the spatially distant κ clusters is nonrandom. Although both split and germline-joined κ genes are expressed, the latter are prominent in young animals and wane with age. We speculate that, in the shark, the differential activation of the multiple isotypes can be advantageously used in receptor editing.
An Overview of the Change Management Process and Examples of Software to Help Organizations Effectively Manage Change
Authors: Santos Noema “Amy” , Quilliam Will 
Published: September 2015

AbstractEvery organization undergoes change on a continual basis and must understand how to manage the change process. This article overviews change management and discusses software packages and other tools that can help organizations manage the inevitable changes which occur frequently. It also examines risks and control objectives associated with change. It concludes that organizations often overlook proper change management techniques and can benefit by the ideas discussed in this article.
Analysis of Intellectual Capital Diclosure Practises: Empirical Study on Services Companies Listed on Indonesia Stock Exchange
Authors: Soebyakto Bambang Bemby , Agustina Mira , Mukhtaruddin  
Published: September 2015

AbstractIntegrated Reporting provides a report that fully integrates financial and non-financial information company. One category of integrated reporting is intellectual capital. It is a voluntary disclosure contained in the company's annual report. The purpose of this study is to analyze the practice of Intellectual Capital Disclosure (ICD) in service companies listed in Indonesia Stock Exchange and empirically examine the effect of corporate governance is proxied by the concentration of ownership, firm size proxied by total assets, the level of profitability is proxied by Return on Assets, leverage, and company listing age on the Stock Exchange on ICD.Samples companies in this study are a service company listed in Indonesia Stock Exchange period 2009-2013. The sampling technique is using purposive sampling method. Based on the established criteria, the company sampled 131 companies. This study uses panel data analysis.The results of this study indicate that the level of ICD in Services Company listed on the Indonesia Stock Exchange is still low. The results of empirical testing in this study indicate that corporate governance, firm size, profitability, leverage, and a listing of companies on the Stock Exchange simultaneously have significant affect to ICD. Partially firm size, profitability, and company listing age on the Stock Exchange have significant effect on ICD, while good corporate governance and leverage levels have no significant effect on ICD.
Mapping RNA‐seq Reads with STAR
Authors: Dobin Alexander , Gingeras Thomas R. 
Published: September 2015

AbstractMapping of large sets of high‐throughput sequencing reads to a reference genome is one of the foundational steps in RNA‐seq data analysis. The STAR software package performs this task with high levels of accuracy and speed. In addition to detecting annotated and novel splice junctions, STAR is capable of discovering more complex RNA sequence arrangements, such as chimeric and circular RNA. STAR can align spliced sequences of any length with moderate error rates, providing scalability for emerging sequencing technologies. STAR generates output files that can be used for many downstream analyses such as transcript/gene expression quantification, differential gene expression, novel isoform reconstruction, and signal visualization. In this unit, we describe computational protocols that produce various output files, use different RNA‐seq datatypes, and utilize different mapping strategies. STAR is open source software that can be run on Unix, Linux, or Mac OS X systems. © 2015 by John Wiley & Sons, Inc.
Using PepExplorer to Filter and Organize De Novo Peptide Sequencing Results
Authors: da Veiga Leprevost Felipe , Barbosa Valmir C. , Carvalho Paulo Costa 
Published: September 2015

AbstractPepExplorer aids in the biological interpretation of de novo sequencing results; this is accomplished by assembling a list of homolog proteins obtained by aligning results from widely adopted de novo sequencing tools against a target‐decoy sequence database. Our tool relies on pattern recognition to ensure that the results satisfy a user‐given false‐discovery rate (FDR). For this, it employs a radial basis function neural network that considers the precursor charge states, de novo sequencing scores, the peptide lengths, and alignment scores. PepExplorer is recommended for studies addressing organisms with no genomic sequence available. PepExplorer is integrated into the PatternLab for proteomics environment, which makes available various tools for downstream data analysis, including the resources for quantitative and differential proteomics. © 2015 by John Wiley & Sons, Inc.