bluuebunny/crossref_metadata_2025_split huggingface dataset:
The predicted secretome and transmembranome of the poultry red mite Dermanyssus gallinae
Authors: Schicht Sabine , Qi Weihong , Poveda Lucy , Strube Christina 
Published: September 2013

AbstractBackgroundThe worldwide distributed hematophagous poultry red miteDermanyssus gallinae(De Geer, 1778) is one of the most important pests of poultry. Even though 35 acaricide compounds are available, control ofD. gallinaeremains difficult due to acaricide resistances as well as food safety regulations. The current study was carried out to identify putative excretory/secretory (pES) proteins ofD. gallinaesince these proteins play an important role in the host-parasite interaction and therefore represent potential targets for the development of novel intervention strategies. Additionally, putative transmembrane proteins (pTM) ofD. gallinaewere analyzed as representatives of this protein group also serve as promising targets for new control strategies.MethodsD. gallinaepES and pTM protein prediction was based on putative protein sequences of whole transcriptome data which was parsed to different bioinformatical servers (SignalP, SecretomeP, TMHMM and TargetP). Subsequently, pES and pTM protein sequences were functionally annotated by different computational tools.ResultsComputational analysis of theD. gallinaeproteins identified 3,091 pES (5.6%) and 7,361 pTM proteins (13.4%). A significant proportion of pES proteins are considered to be involved in blood feeding and digestion such as salivary proteins, proteases, lipases and carbohydrases. The cysteine proteases cathepsin D and L as well as legumain, enzymes that cleave hemoglobin during blood digestion of the near related ticks, represented 6 of the top-30 BLASTP matches of the poultry red mite’s secretome. Identified pTM proteins may be involved in many important biological processes including cell signaling, transport of membrane-impermeable molecules and cell recognition. Ninjurin-like proteins, whose functions in mites are still unknown, represent the most frequently occurring pTM.ConclusionThe current study is the first providing a mite’s secretome as well as transmembranome and provides valuable insights intoD. gallinaepES and pTM proteins operating in different metabolic pathways. Identifying a variety of molecules putatively involved in blood feeding may significantly contribute to the development of new therapeutic targets or vaccines against this poultry pest.
Expectantly waiting: A survey of thyroid surgery wait times among Canadian Otolaryngologists
Authors: Brake Maria , Moore Paige , Taylor S Mark , Trites Jonathan , Murray Scott , Hart Rob 
Published: September 2013

Background Our objective is to highlight discrepancies between actual wait times and perceived appropriate wait times for various thyroid pathologies among Otolaryngology- Head and Neck Surgeons in Canada; and to identify specific diagnoses/pathologies where wait times could be improved. Methods A questionnaire was distributed to all practicing CSO-HNS members. Questions focused on actual wait times for initial consults and surgery within individual practices, in the setting of various thyroid pathologies. Respondents were also asked to state wait times that they felt were appropriate for each scenario. Wilcoxon signed-rank tests were performed to determine statistically significant differences between actual and appropriate wait times. Results For most scenarios, the actual wait times were significantly longer than most physicians felt were appropriate; these scenarios included time to initial consult for undiagnosed nodules, time to surgery for confirmed malignancies, and time to completion thyroidectomy for surgically confirmed malignancies. Conclusions Wait times for thyroid consults and surgeries in Canada are longer than physicians feel are appropriate. The authors hope that this survey may spur a move towards a national consensus on appropriate wait times for the treatment of thyroid pathology.
Recent advances in application of chitosan in fuel cells
Authors: Vaghari Hamideh , Jafarizadeh-Malmiri Hoda , Berenjian Aydin , Anarjan Navideh 
Published: September 2013

Abstract
Fuel cells are electrochemical devices which convert chemical energy into electrical energy. Fuel cells have attracted attention due to their potential as a promising alternative to traditional power sources. More recently, efficient and environmentally benign biopolymer “chitosan” have been extensively investigated as a novel material for its application in fuel cells. This biopolymer can be used in both membrane electrolyte and electrode in various fuel cells such as alkaline polymer electrolyte fuel cells, direct methanol fuel cells and biofuel cells. This review provides an overview of main available fuel cells following by application of chitosan as novel biopolymer in fuel cells technology. Recent achievements are included and recommendations are also given for areas of future research.
Handgrip and quadriceps muscle endurance testing in young adults
Authors: White Ciara , Dixon Kimberley , Samuel Dinesh , Stokes Maria 
Published: September 2013

Abstract

Background
Grip strength is widely used for estimating whole body strength but there is a lack of information relating to grip endurance. Comparison between endurance of different muscle groups has received little attention. The main aim of the present study was to determine the endurance characteristics of hand grip and quadriceps muscles in healthy young adults and then to examine the association between fatigability of the two muscle groups.

Methods
Twenty one healthy participants (8 males and 13 females) aged 18–35 years were studied. A maximal intermittent endurance test, consisting of 12 isometric contractions held for 3 seconds separated by 5 second rest periods, was utilised to measure muscle endurance. A Biodex isokinetic dynamometer and Jamar dynamometer were used to assess quadriceps and hand grip respectively. The mean of first (M1) and last (M2) three repetitions was calculated. Fatigue index values were calculated for both muscle groups by the 1st peak torque (PT) minus the last (12th) PT, divided by the 1st PT multiplied by 100.

Results
Quadriceps torque (M1:197.3 ± 65.2 Nm; M2:163.1 ± 47.6 Nm) and grip strength (M1:33.6 ± 9.9 Kg; M2:25.2 ± 8.1 Kg) both declined significantly during the 12 repetitions (p < 0.05). Hand grip showed a significantly higher mean fatigue index of 30% compared to 18% in the quadriceps (p < 0.05).

Conclusions
Quadriceps showed better fatigability than hand grip. The findings therefore indicate caution against using grip endurance as a surrogate measure of quadriceps endurance. Further research is warranted to confirm observed differences between genders and to study endurance in different age groups.
Low-dose protocol of the spiral CT in orthodontics: comparative evaluation of entrance skin dose with traditional X-ray techniques
Authors: Cordasco Giancarlo , Portelli Marco , Militi Angela , Nucera Riccardo , Giudice Antonino Lo , Gatto Elda , Lucchese Alessandra 
Published: September 2013

Abstract

Background
The aim of this study was to evaluate the amount of radiation doses absorbed by soft tissues (entrance skin dose) with a low-dose spiral computed tomography (CT) protocol compared to conventional X-ray techniques commonly used in orthodontics.

Methods
The amount of skin dose has been evaluated using a tissue-equivalent head-neck radiotherapy humanoid phantom with thermoluminescent dosimeters placed at the level of eye lens, parotid glands, and thyroid glands. CT images have been taken using a Sensation 16 Siemens CT scan and a low-dose protocol (15 mAs, 1 pitch, 2.5 mGy (CTDIvol), 80 kV, 1-mm slice thickness).

Results
The difference in image quality between traditional X-ray techniques and low-dose spiral CT was statistically significant (P < 0.05). The difference in mean absorbed dose instead was not statistically significant.

Conclusions
Our protocol allows a more accurate orthodontic diagnosis without an increase of radiological risk for the patients in comparison to traditional X-ray techniques.
Bacterial lipopolysaccharides form procollagen-endotoxin complexes that trigger cartilage inflammation and degeneration: implications for the development of rheumatoid arthritis
Authors: Lorenz Wolfgang , Buhrmann Constanze , Mobasheri Ali , Lueders Cora , Shakibaei Mehdi 
Published: September 2013

Abstract
Introduction
We have previously reported that bacterial toxins, especially endotoxins such as lipopolysaccharides (LPS), might be important causative agents in the pathogenesis of rheumatoid arthritis (RA) in an in vitro model that simulates the potential effects of residing in damp buildings. Since numerous inflammatory processes are linked with the nuclear factor-κB (NF-κB), we investigated in detail the effects of LPS on the NF-κB pathway and the postulated formation of procollagen-endotoxin complexes.

Methods
An in vitro model of human chondrocytes was used to investigate LPS-mediated inflammatory signaling.

Results
Immunoelectron microscopy revealed that LPS physically interact with collagen type II in the extracellular matrix (ECM) and anti-collagen type II significantly reduced this interaction. BMS-345541 (a specific inhibitor of IκB kinase (IKK)) or wortmannin (a specific inhibitor of phosphatidylinositol 3-kinase (PI-3K)) inhibited the LPS-induced degradation of the ECM and apoptosis in chondrocytes. This effect was completely inhibited by combining BMS-345541 and wortmannin. Furthermore, BMS-345541 and/or wortmannin suppressed the LPS-induced upregulation of catabolic enzymes that mediate ECM degradation (matrix metalloproteinases-9, -13), cyclooxygenase-2 and apoptosis (activated caspase-3). These proteins are regulated by NF-κB, suggesting that the NF-κB and PI-3K pathways are involved in LPS-induced cartilage degradation. The induction of NF-κB correlated with activation of IκBα kinase, IκBα phosphorylation, IκBα degradation, p65 phosphorylation and p65 nuclear translocation. Further upstream, LPS induced the expression of Toll-like receptor 4 (TLR4) and bound with TLR4, indicating that LPS acts through TLR4.

Conclusion
These results suggest that molecular associations between LPS/TLR4/collagen type II in chondrocytes upregulate the NF-κB and PI-3K signaling pathways and activate proinflammatory activity.
A genome-wide association study of chemotherapy-induced alopecia in breast cancer patients
Authors: Chung Suyoun , Low Siew-Kee , Zembutsu Hitoshi , Takahashi Atsushi , Kubo Michiaki , Sasa Mitsunori , Nakamura Yusuke 
Published: September 2013

Abstract
Introduction
Chemotherapy-induced alopecia is one of the most common adverse events caused by conventional cytotoxic chemotherapy, yet there has been very little progress in the prevention or treatment of this side effect. Although this is not a life-threatening event, alopecia is very psychologically difficult for many women to manage. In order to improve the quality of life for these women, it is important to elucidate the molecular mechanisms of chemotherapy-induced alopecia and develop ways to effectively prevent and/or treat it. To identify the genetic risk factors associated with chemotherapy-induced alopecia, we conducted a genome-wide association study (GWAS) using DNA samples from breast cancer patients who were treated with chemotherapy.

Methods
We performed a case-control association study of 303 individuals who developed grade 2 alopecia, and compared them with 880 breast cancer patients who did not show hair loss after being treated with conventional chemotherapy. In addition, we separately analyzed a subset of patients who received specific combination therapies by GWASs and applied the weighted genetic risk scoring (wGRS) system to investigate the cumulative effects of the associated SNPs.

Results
We identified an SNP significantly associated with drug-induced grade 2 alopecia (rs3820706 in CACNB4 (calcium channel voltage-dependent subunit beta 4) on 2q23, P = 8.13 × 10-9, OR = 3.71) and detected several SNPs that showed some suggestive associations by subgroup analyses. We also classified patients into four groups on the basis of wGRS analysis and found that patients who classified in the highest risk group showed 443 times higher risk of antimicrotubule agents-induced alopecia than the lowest risk group.

Conclusions
Our study suggests several associated genes and should shed some light on the molecular mechanism of alopecia in chemotherapy-treated breast cancer patients and hopefully will contribute to development of interventions that will improve the quality of life (QOL) of cancer patients.
Even Mild Hyperlactatemia Is Associated with Increased Mortality in Critically Ill Patients
Authors: Rishu Asgar H , Khan Raymond , Al-Dorzi Hasan M , Tamim Hani M , Al-Qahtani Saad , Al-Ghamdi Ghassan , Arabi Yaseen M 
Published: September 2013

Abstract
Introduction
The clinical significance of elevation of lactate levels within the reference range is not well studied. The objective of this study was to determine the best cutoff threshold for serum lactate within the reference range (0.01 to 2.00 mM) that best discriminated between survivors and nonsurvivors of critical illness and to examine the association between relative hyperlactatemia (lactate above the identified threshold) and mortality.

Methods
This was a retrospective cohort study of adult patients admitted to the medical-surgical intensive care unit (ICU) of a tertiary care academic center. Youden index was calculated to identify the best lactate cutoff threshold that discriminated between survivors and nonsurvivors. Patients with lactate above the identified threshold were defined as having relative hyperlactatemia. Multivariate logistic regression, adjusting for baseline variables, was performed to determine the relationship between the above two ranges of lactate levels and mortality. In addition, a test of interaction was performed to assess the effect of selected subgroups on the association between relative hyperlactatemia and hospital mortality.

Results
During the study period, 2,157 patients were included in the study with mean lactate of 1.3 ± 0.4 mM, age of 55.1 ± 20.3 years, and acute physiology and chronic health evaluation (APACHE) II score of 22.1 ± 8.2. Vasopressors were required in 42.4%. Lactate of 1.35 mM was found to be the best cutoff threshold for the whole cohort. Relative hyperlactatemia was associated with increased hospital mortality (adjusted odds ratio (aOR), 1.60, 95% confidence interval (CI) 1.29 to 1.98), and ICU mortality (aOR, 1.66; 95% CI, 1.26 to 2.17) compared with a lactate level of 0.01 to 1.35 mM. This association was consistent among all examined subgroups.

Conclusions
Relative hyperlactatemia (lactate of 1.36 to 2.00 mM) within the first 24 hours of ICU admission is an independent predictor of hospital and ICU mortality in critically ill patients.
Systemic endotoxin activity correlates with clot formation: an observational study in patients with early systemic inflammation and sepsis
Authors: Koch Alexander , Meesters Michael Isaäc , Scheller Bertram , Boer Christa , Zacharowski Kai 
Published: September 2013

Abstract
Introduction
Inflammation and coagulation are closely linked, and both can be triggered by endotoxin. Thrombelastometry and impedance aggregometry are of diagnostic and predictive value in critically ill patients. In this observational study we investigated the correlation of endotoxin activity with thrombelasometric and aggregometric variables in patients with systemic inflammation.

Methods
Based on a daily screening on a tertiary academic surgical ICU, patients, as soon as they fulfilled two or more criteria for systemic inflammatory response syndrome (SIRS), were included. In whole blood we performed endotoxin activity (EA) assay, thrombelastometry (ROTEM®) and impendance aggregometry (Multiplate®).

Results
In total, 49 patients were included with a broad spread of EA levels of (median (minimum to maximum)) 0.27 (0.01 to 0.72), allowing expedient correlative analysis. Clot formation time (CFT) (263 s (60 to 1,438 s)) and clotting time (CT) (1,008 s (53 to 1,481 s)) showed a significant negative correlation with EA level (r = -0.38 (P < 0.005) and r = -0.29 (P < 0.05)). Positive correlations were found for alpha-angle (50° (17 to 78°), r = 0.40 (P < 0.005)) and maximum clot firmness (MCF) (55 mm (5/76), r = 0.27 (P < 0.05)). No significant correlations were found between Lysis Index at 60 minutes (LI60) and EA levels. There was no correlation between EA level and aggregometric values, or classical coagulation parameters.

Conclusions
In patients with systemic inflammation, increasing endotoxin concentrations correlate with increased clot formation.
Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data
Authors: Rapaport Franck , Khanin Raya , Liang Yupu , Pirun Mono , Krek Azra , Zumbo Paul , Mason Christopher E , Socci Nicholas D , Betel Doron 
Published: September 2013

AbstractA large number of computational methods have been developed for analyzing differential gene expression in RNA-seq data. We describe a comprehensive evaluation of common methods using the SEQC benchmark dataset and ENCODE data. We consider a number of key features, including normalization, accuracy of differential expression detection and differential expression analysis when one condition has no detectable expression. We find significant differences among the methods, but note that array-based methods adapted to RNA-seq data perform comparably to methods designed for RNA-seq. Our results demonstrate that increasing the number of replicate samples significantly improves detection power over increased sequencing depth.
The effects of high-fat diet, branched-chain amino acids and exercise on female C57BL/6 mouse Achilles tendon biomechanical properties
Authors: Boivin G. P. , Platt K. M. , Corbett J. , Reeves J. , Hardy A. L. , Elenes E. Y. , Charnigo R. J. , Hunter S. A. , Pearson K. J. 
Published: September 2013

Objectives The goals of this study were: 1) to determine if high-fat diet (HFD) feeding in female mice would negatively impact biomechanical and histologic consequences on the Achilles tendon and quadriceps muscle; and 2) to investigate whether exercise and branched-chain amino acid (BCAA) supplementation would affect these parameters or attenuate any negative consequences resulting from HFD consumption. Methods We examined the effects of 16 weeks of 60% HFD feeding, voluntary exercise (free choice wheel running) and BCAA administration in female C57BL/6 mice. The Achilles tendons and quadriceps muscles were removed at the end of the experiment and assessed histologically and biomechanically. Results HFD feeding significantly decreased the Achilles tendon modulus without histological alterations. BCAA administration significantly decreased the stiffness of Achilles tendons in the exercised normal diet mice. Exercise partially ameliorated both the weight gain and glucose levels in the HFD-fed mice, led to a significant decrease in the maximum load of the Achilles tendon, and an increase in the average fibril diameter of the quadriceps femoris muscle. There were significant correlations between body weight and several biomechanical properties, demonstrating the importance of controlling obesity for maintaining healthy tendon properties. Conclusions In summary, this study showed a significant impact of obesity and body weight on tendon biomechanical properties with limited effects of exercise and BCAAs. Cite this article: Bone Joint Res 2013;2:186–92.
Three-dimensional assessment of hand outcome
Authors: Pearl RA , Belcher HJCR 
Published: September 2013

Introduction Patient reported outcome measures are central to National Health Service quality of care assessments. This study investigated the benefit of elective hand surgery by the simultaneous analysis of pain, function and appearance, using a three-dimensional (3D) graphical model for evaluating and presenting outcome. Methods A total of 188 patients scheduled for surgery completed pre- and postoperative questionnaires grading the severity of their pain, dysfunction and deformity of their hand(s). Scores were plotted on a 3D graph to demonstrate the degree of ‘normalisation’ following surgery. Results Surgical groups included: nerve compression (n=53), Dupuytren’s disease (n=51), trigger finger (n=20), ganglion (n=17) or other lump (n=21), trapeziometacarpal joint osteoarthritis (n=10), rheumatoid disease (n=5) and other pathology (n=13). A significant improvement towards normality was seen after surgery in each group except for patients with rheumatoid disease. Conclusions This study provides a simple, visual representation of hand surgery outcome by plotting patient scores for pain, function and appearance simultaneously on a 3D graph.
Diplomacy of the Kurdish territorial nation
Authors: Talhami Ghada Hashem 
Published: September 2013

Abstract
This article argues that focusing on the foreign policy choices of the Kurdish leadership since Mulla Mustafa Barzani began seeking autonomy within Iraq will shed light on the strengths and weaknesses of the Kurdish national movement. This essay sketches the rise of the Kurdish-American and Kurdish-Israeli alliances which aided the Kurds during the American occupation of Iraq. Due to Kurdish desire to consolidate their control over the hydrocarbon resources of their region, Iraq and the Kurdish Regional Government find themselves locked in a dangerous struggle, which involves Turkey, Iran and Israel. Particular attention is paid to the refractory nature of these alliances and the implications of Kurdish Iraqi autonomy to the Kurdish communities of the region.
Change or more of the same? Obama and Iraq
Authors: Terry Janice J. 
Published: September 2013

Abstract
This article traces the changes in US foreign policy towards Iraq under the Obama presidency. Although Obama adopted a less aggressive and more cautious approach to Iraq than that of George W. Bush, the long-term interests and goals of the United States in Iraq remained much the same. In the ongoing struggle between the central government in Baghdad and the Kurds the United States is caught in the middle while trying to appease both sides. In addition, the involvement of the U.S. petroleum industry in Iraq is of particular importance to the United States and this long-term interest remains the same whether a Republican or Democrat is in the White House.
The United States’ withdrawal from Iraq: Challenges and results
Authors: Aljanabi Basim Karim Swidan 
Published: September 2013

Abstract
This essay examines the internal repercussions for Iraq of the US withdrawal. They can be summarized as the lack of a national political agenda that could lead to a unified Iraqi state; the absence of an Iraqi-centered army with national sovereignty as its main concern; failure to resolve conflicts between the Iraqi center and its periphery about a number of issues, including oil and gas; lack of clarity in the Constitution, especially paragraphs that deal with sectarianism and ethnic quotas; and a failure to resolve administrative and financial corruption.
Site specificity in the age of intermediality (with thanks to Michael Snow)
Authors: Marchessault Janine 
Published: September 2013

Abstract
This article addresses the materialist screen works of Canadian artist Michael Snow. It argues that Snow’s lifelong experimentations with different media technologies have always encompassed a rigorous and precise understanding of the phenomenology of the different viewing situations in which his works are seen. Two aspects of Snow’s practice are singled out as inherently connected: medium specificity and audiency. Snow’s artworks provide us with unique opportunities to grasp the complexities of changing forms of intermediality and spectatorship at a time when media are more fluid and ephemeral than ever before.