Effects of nicotine administration in rats on MMP2 and VEGF levels in periodontal membrane

Background: Nicotine is associated with increased incidence of periodontal disease and poor response to therapy. This article aimed at identifying the expression of matrix metalloproteinases 2 (MMPs2) and vascular endothelial growth factor (VEGF) proteins on extracellular matrix, fibrous distribution and angiogenetic development in periodontitis caused by nicotine effects on periodontal membrane.Materials and methods: In this experimental study, rats were divided into nicotine and control groups. While the rats in the nicotine group (n = 6) were administered 2 mg/kg nicotine sulphate for 28 days, the animals in the control group (n = 6) were only administered 1.5 mL physiologic saline solution subcutaneously for 28 days.Results: Histological sections were prepared and immunohistochemically stained for MMP2 and VEGF. The sections stained with Trichrome-Masson were observed under light microscope. VEGF and MMP2 immunoreactivity of periodontal gingiva and dentin was assessed by immunohistochemical staining.Conclusions: Nicotine reduces MMP production, disrupts collagen synthesis and causes periodontitis. We observed that nicotine increases periodontitis by disrupting periodontal membrane and prevents tooth to anchor in dental alveoli by disrupting epithelial structure

Investigation of antioxidant effects of rosmarinic acid on liver, lung and kidney in rats: a biochemical and histopathological study

Background: The aim of the study was to investigate the protective effects of rosmarinic acid in rats exposed to hepatic ischaemia/reperfusion (I/R) injury. Materials and methods: Thirty-two rats were randomly classified into four groups of 8 rats each: laparotomy without medication, rosmarinic acid (dose of 50 mg/kg via oral gavage) followed by laparotomy, laparotomy followed by hepatic I/R, and hepatic I/R with rosmarinic acid. Serum aspartate aminotransferase, alaninę aminotransferase, and malondialdehyde levels and total oxidant activity and total antioxidant capacity levels of the liver, lung, and kidney were assessed. The histopathologic assessment was also performed. Results: Rosmarinic acid significantly reduced liver function test parameters and decreased oxidative stress and abnormal histopathologic findings in the liver. The oxidative stress in the lung significantly increased in the I/R group but significantly decreased in the I/R + rosmarinic acid group due to the addition of rosmarinic acid. Rosmarinic acid led to no reduction in oxidative stress in kidney following hepatic I/R injury. There were no statistically significant differences among the groups regarding histopathologic changes in kidney and lung sections. Conclusions: Rosmarinic acid has antioxidant properties and is an effective hepatoprotective agent. However, although rosmarinic acid provides useful effects in the lung by increasing antioxidant capacity and reducing oxidative stress after I/R injury, it does not ameliorate histopathologic changes. These findings suggest that rosmarinic acid is likely to provide favourable outcomes in the treatment of hepatic I/R injury

The effect of anesthesia type on stress hormone response: Comparison of general versus epidural anesthesia

Aim: The aim of this study was to investigate the effect of different types of anesthesia on stress hormones.Materials and Methods: The study was included 60 ASAI-II cases scheduled for major lower extremity surgery. The cases were randomized into 2  groups: The EA group was administered epidural anesthesia and the GA group was administered standard general anesthesia. In order to evaluate the surgical trauma - related stress response, CRP, TSH, cortisol, and fasting blood sugar(FBS) levels were measured preoperatively, 30 min after surgical incision, and 24 h post surgery.Results: Between-group comparisons; Preoperative values were not  significantly different between the groups.(P > 0,05) Pulse rate and cortisol values significantly higher in general group at 30 min. (P < 0,05), and the FBS values were significantly higher in the epidural group at 24 h.(P < 0,05) There were not found differences for other parameters at evaluation times.Conclusion: No differences were observed between the two anesthesia methods, in terms of minimizing the stress response due to surgical trauma during major low extremity surgery.Key words: Epidural anesthesia, general anesthesia, stress hormone

A content-linking-context model for “notice-and-takedown” procedures

The US Digital Millennium Copyright Act (DMCA) of 1998 adopted a notice-and-take-down procedure to help tackle alleged online infringements through online service providers’ actions. The European Directive 2000/31/EC (e-Commerce Directive) introduced similar liability exemptions, but did not specify any take-down procedure. Many intermediary (host, and online search engine) service providers even in Europe have followed this notice-and-take-down procedure to enable copyright owners to issue notices to take down allegedly infringing Web resources. However, the accuracy of take-down is not known, and notice receivers do not reveal clear information about how they check the legitimacy of these requests, about whether and how they check the lawfulness of allegedly infringing content, or what criteria they use for these actions. In this paper, we use Google’s Transparency Report as the benchmark to investigate the information content of take-down notices and the accuracy of the resulting take-downs of allegedly infringing Web resources. The analysis of copyright infringement is limited to the five scenarios most frequently encountered in our study of Web resources. Based on our investigation, we propose a Content-Linking-Context (CLC) model of the criteria to be considered by intermediary service providers to achieve more accurate take-down

Site selection of the Colombian antarctic research station based on fuzzy-topsis algorithm

By 2025 the Republic of Colombia aims to be an advisory member of the Antarctic Treaty System (ATS) and the installation of a scientific station is necessary to upscale the scientific capabilities. The aim of this paper is showing the results of the implementation of a Fuzzy TOPSIS algorithm for site selection of the Colombian Antarctic Scientific Station. A three-phase methodology was AQ1 proposed, and the obtained results allowed to identify the optimum location for the station, considering key success factors and regulatory constraints

IL-6 mediated JAK/STAT3 signaling pathway in cancer patients with cachexia

CONCLUSION: STAT3 may be considered as a therapeutic target for cachectic patients with gastric, lung and breast cancer. Furthermore, IL-6 mediates STAT3 activation in cachectic gastric and breast cancer patients (Tab. 5, Fig. 2, Ref. 62)

A Hybrid Fuzzy Multi-criteria Decision Making Model to Evaluate the Overall Performance of Public Emergency Departments: A Case Study

[EN] Performance evaluation is relevant for supporting managerial decisions related to the improvement of public emergency departments (EDs). As different criteria from ED context and several alternatives need to be considered, selecting a suitable Multicriteria Decision-Making (MCDM) approach has become a crucial step for ED performance evaluation. Although some methodologies have been proposed to address this challenge, a more complete approach is still lacking. This paper bridges this gap by integrating three potent MCDM methods. First, the Fuzzy Analytic Hierarchy Process (FAHP) is used to determine the criteria and sub-criteria weights under uncertainty, followed by the interdependence evaluation via fuzzy Decision-Making Trial and Evaluation Laboratory(FDEMATEL). The fuzzy logic is merged with AHP and DEMATEL to illustrate vague judgments. Finally, the Technique for Order of Preference by Similarity to Ideal Solution (TOPSIS) is used for ranking EDs. This approach is validated in a real 3-ED cluster. The results revealed the critical role of Infrastructure (21.5%) in ED performance and the interactive nature of Patient safety (C+R =12.771). Furthermore, this paper evidences the weaknesses to be tackled for upgrading the performance of each ED.Ortiz-Barrios, M.; Alfaro Saiz, JJ. (2020). A Hybrid Fuzzy Multi-criteria Decision Making Model to Evaluate the Overall Performance of Public Emergency Departments: A Case Study. International Journal of Information Technology & Decision Making. 19(6):1485-1548. https://doi.org/10.1142/S0219622020500364S14851548196Lord, K., Parwani, V., Ulrich, A., Finn, E. B., Rothenberg, C., Emerson, B., … Venkatesh, A. K. (2018). Emergency department boarding and adverse hospitalization outcomes among patients admitted to a general medical service. The American Journal of Emergency Medicine, 36(7), 1246-1248. doi:10.1016/j.ajem.2018.03.043Sørup, C. M., Jacobsen, P., & Forberg, J. L. (2013). 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(2018). A Fuzzy AHP–TOPSIS-Based Group Decision-Making Approach to IT Personnel Selection. International Journal of Fuzzy Systems, 20(5), 1576-1591. doi:10.1007/s40815-018-0474-7CHEN, M.-F., TZENG, G.-H., & TANG, T.-I. (2005). FUZZY MCDM APPROACH FOR EVALUATION OF EXPATRIATE ASSIGNMENTS. International Journal of Information Technology & Decision Making, 04(02), 277-296. doi:10.1142/s0219622005001520Gul, M., Celik, E., Gumus, A. T., & Guneri, A. F. (2016). Emergency department performance evaluation by an integrated simulation and interval type-2 fuzzy MCDM-based scenario analysis. European J. of Industrial Engineering, 10(2), 196. doi:10.1504/ejie.2016.075846Jovčić, Průša, Dobrodolac, & Švadlenka. (2019). A Proposal for a Decision-Making Tool in Third-Party Logistics (3PL) Provider Selection Based on Multi-Criteria Analysis and the Fuzzy Approach. Sustainability, 11(15), 4236. doi:10.3390/su11154236Saaty, T. L., & Vargas, L. G. (2012). 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K., Govindan, K., Antucheviciene, J., & Turskis, Z. (2016). Hybrid multiple criteria decision-making methods: a review of applications for sustainability issues. Economic Research-Ekonomska Istraživanja, 29(1), 857-887. doi:10.1080/1331677x.2016.1237302Lolli, F., Balugani, E., Ishizaka, A., Gamberini, R., Butturi, M. A., Marinello, S., & Rimini, B. (2019). On the elicitation of criteria weights in PROMETHEE-based ranking methods for a mobile application. Expert Systems with Applications, 120, 217-227. doi:10.1016/j.eswa.2018.11.030De Almeida Filho, A. T., Clemente, T. R. N., Morais, D. C., & de Almeida, A. T. (2018). Preference modeling experiments with surrogate weighting procedures for the PROMETHEE method. European Journal of Operational Research, 264(2), 453-461. doi:10.1016/j.ejor.2017.08.006Sun, G., Guan, X., Yi, X., & Zhou, Z. (2018). An innovative TOPSIS approach based on hesitant fuzzy correlation coefficient and its applications. Applied Soft Computing, 68, 249-267. doi:10.1016/j.asoc.2018.04.004Frazão, T. D. C., Camilo, D. G. G., Cabral, E. L. S., & Souza, R. P. (2018). Multicriteria decision analysis (MCDA) in health care: a systematic review of the main characteristics and methodological steps. BMC Medical Informatics and Decision Making, 18(1). doi:10.1186/s12911-018-0663-1Ortiz-Barrios, M. A., Herrera-Fontalvo, Z., Rúa-Muñoz, J., Ojeda-Gutiérrez, S., De Felice, F., & Petrillo, A. (2018). An integrated approach to evaluate the risk of adverse events in hospital sector. Management Decision, 56(10), 2187-2224. doi:10.1108/md-09-2017-0917Al Salem, A. A., & Awasthi, A. (2018). Investigating rank reversal in reciprocal fuzzy preference relation based on additive consistency: Causes and solutions. Computers & Industrial Engineering, 115, 573-581. doi:10.1016/j.cie.2017.11.027Aires, R. F. de F., & Ferreira, L. (2019). A new approach to avoid rank reversal cases in the TOPSIS method. Computers & Industrial Engineering, 132, 84-97. doi:10.1016/j.cie.2019.04.023Emrouznejad, A., & Yang, G. (2018). A survey and analysis of the first 40 years of scholarly literature in DEA: 1978–2016. Socio-Economic Planning Sciences, 61, 4-8. doi:10.1016/j.seps.2017.01.008Arya, A., & Yadav, S. P. (2017). Development of FDEA Models to Measure the Performance Efficiencies of DMUs. International Journal of Fuzzy Systems, 20(1), 163-173. doi:10.1007/s40815-017-0325-yMufazzal, S., & Muzakkir, S. M. (2018). A new multi-criterion decision making (MCDM) method based on proximity indexed value for minimizing rank reversals. Computers & Industrial Engineering, 119, 427-438. doi:10.1016/j.cie.2018.03.045Kaliszewski, I., & Podkopaev, D. (2016). Simple additive weighting—A metamodel for multiple criteria decision analysis methods. Expert Systems with Applications, 54, 155-161. doi:10.1016/j.eswa.2016.01.042Mousavi-Nasab, S. H., & Sotoudeh-Anvari, A. (2018). A new multi-criteria decision making approach for sustainable material selection problem: A critical study on rank reversal problem. Journal of Cleaner Production, 182, 466-484. doi:10.1016/j.jclepro.2018.02.062Chen, Z., Ming, X., Zhang, X., Yin, D., & Sun, Z. (2019). A rough-fuzzy DEMATEL-ANP method for evaluating sustainable value requirement of product service system. Journal of Cleaner Production, 228, 485-508. doi:10.1016/j.jclepro.2019.04.145Jumaah, F. M., Zadain, A. A., Zaidan, B. B., Hamzah, A. K., & Bahbibi, R. (2018). Decision-making solution based multi-measurement design parameter for optimization of GPS receiver tracking channels in static and dynamic real-time positioning multipath environment. Measurement, 118, 83-95. doi:10.1016/j.measurement.2018.01.011Singh, A., & Prasher, A. (2017). Measuring healthcare service quality from patients’ perspective: using Fuzzy AHP application. Total Quality Management & Business Excellence, 30(3-4), 284-300. doi:10.1080/14783363.2017.1302794Otay, İ., Oztaysi, B., Cevik Onar, S., & Kahraman, C. (2017). Multi-expert performance evaluation of healthcare institutions using an integrated intuitionistic fuzzy AHP&DEA methodology. Knowledge-Based Systems, 133, 90-106. doi:10.1016/j.knosys.2017.06.028Awasthi, A., Govindan, K., & Gold, S. (2018). Multi-tier sustainable global supplier selection using a fuzzy AHP-VIKOR based approach. International Journal of Production Economics, 195, 106-117. doi:10.1016/j.ijpe.2017.10.013Gul, M., Guneri, A. F., & Nasirli, S. M. (2018). A fuzzy-based model for risk assessment of routes in oil transportation. International Journal of Environmental Science and Technology, 16(8), 4671-4686. doi:10.1007/s13762-018-2078-zKazancoglu, Y., Kazancoglu, I., & Sagnak, M. (2018). Fuzzy DEMATEL-based green supply chain management performance. Industrial Management & Data Systems, 118(2), 412-431. doi:10.1108/imds-03-2017-0121Abdullah, L., & Zulkifli, N. (2015). Integration of fuzzy AHP and interval type-2 fuzzy DEMATEL: An application to human resource management. Expert Systems with Applications, 42(9), 4397-4409. doi:10.1016/j.eswa.2015.01.021Ashtiani, M., & Azgomi, M. A. (2016). A hesitant fuzzy model of computational trust considering hesitancy, vagueness and uncertainty. Applied Soft Computing, 42, 18-37. doi:10.1016/j.asoc.2016.01.023Zyoud, S. H., & Fuchs-Hanusch, D. (2017). A bibliometric-based survey on AHP and TOPSIS techniques. Expert Systems with Applications, 78, 158-181. doi:10.1016/j.eswa.2017.02.016Scholz, S., Ngoli, B., & Flessa, S. (2015). Rapid assessment of infrastructure of primary health care facilities – a relevant instrument for health care systems management. BMC Health Services Research, 15(1). doi:10.1186/s12913-015-0838-8Ivlev, I., Vacek, J., & Kneppo, P. (2015). Multi-criteria decision analysis for supporting the selection of medical devices under uncertainty. European Journal of Operational Research, 247(1), 216-228. doi:10.1016/j.ejor.2015.05.075Kovacs, E., Strobl, R., Phillips, A., Stephan, A.-J., Müller, M., Gensichen, J., & Grill, E. (2018). Systematic Review and Meta-analysis of the Effectiveness of Implementation Strategies for Non-communicable Disease Guidelines in Primary Health Care. Journal of General Internal Medicine, 33(7), 1142-1154. doi:10.1007/s11606-018-4435-5Morley, C., Unwin, M., Peterson, G. M., Stankovich, J., & Kinsman, L. (2018). Emergency department crowding: A systematic review of causes, consequences and solutions. PLOS ONE, 13(8), e0203316. doi:10.1371/journal.pone.0203316Hermann, R. M., Long, E., & Trotta, R. L. (2019). Improving Patients’ Experiences Communicating With Nurses and Providers in the Emergency Department. Journal of Emergency Nursing, 45(5), 523-530. doi:10.1016/j.jen.2018.12.001Hawley, K. L., Mazer-Amirshahi, M., Zocchi, M. S., Fox, E. R., & Pines, J. M. (2015). Longitudinal Trends in U.S. Drug Shortages for Medications Used in Emergency Departments (2001-2014). Academic Emergency Medicine, 23(1), 63-69. doi:10.1111/acem.12838Stang, A. S., Crotts, J., Johnson, D. W., Hartling, L., & Guttmann, A. (2015). Crowding Measures Associated With the Quality of Emergency Department Care: A Systematic Review. Academic Emergency Medicine, 22(6), 643-656. doi:10.1111/acem.12682Chanamool, N., & Naenna, T. (2016). Fuzzy FMEA application to improve decision-making process in an emergency department. Applied Soft Computing, 43, 441-453. doi:10.1016/j.asoc.2016.01.007Farup, P. G. (2015). Are measurements of patient safety culture and adverse events valid and reliable? Results from a cross sectional study. BMC Health Services Research, 15(1). doi:10.1186/s12913-015-0852-xCarter, E. J., Pouch, S. M., & Larson, E. L. (2013). The Relationship Between Emergency Department Crowding and Patient Outcomes: A Systematic Review. Journal of Nursing Scholarship, 46(2), 106-115. doi:10.1111/jnu.12055Ebben, R. H. A., Siqeca, F., Madsen, U. R., Vloet, L. C. M., & van Achterberg, T. (2018). Effectiveness of implementation strategies for the improvement of guideline and protocol adherence in emergency care: a systematic review. BMJ Open, 8(11), e017572. doi:10.1136/bmjopen-2017-017572Innes, G. D., Sivilotti, M. L. A., Ovens, H., McLelland, K., Dukelow, A., Kwok, E., … Chochinov, A. (2018). Emergency overcrowding and access block: A smaller problem than we think. CJEM, 21(2), 177-185. doi:10.1017/cem.2018.446Di Somma, S., Paladino, L., Vaughan, L., Lalle, I., Magrini, L., & Magnanti, M. (2014). Overcrowding in emergency department: an international issue. Internal and Emergency Medicine, 10(2), 171-175. doi:10.1007/s11739-014-1154-8Uthman, O. A., Walker, C., Lahiri, S., Jenkinson, D., Adekanmbi, V., Robertson, W., & Clarke, A. (2018). General practitioners providing non-urgent care in emergency department: a natural experiment. BMJ Open, 8(5), e019736. doi:10.1136/bmjopen-2017-019736Razzak, J. A., Baqir, S. M., Khan, U. R., Heller, D., Bhatti, J., & Hyder, A. A. (2013). Emergency and trauma care in Pakistan: a cross-sectional study of healthcare levels. Emergency Medicine Journal, 32(3), 207-213. doi:10.1136/emermed-2013-202590Dart, R. C., Goldfrank, L. R., Erstad, B. L., Huang, D. T., Todd, K. H., Weitz, J., … Anderson, V. E. (2018). Expert Consensus Guidelines for Stocking of Antidotes in Hospitals That Provide Emergency Care. Annals of Emergency Medicine, 71(3), 314-325.e1. doi:10.1016/j.annemergmed.2017.05.021Mkoka, D. A., Goicolea, I., Kiwara, A., Mwangu, M., & Hurtig, A.-K. (2014). Availability of drugs and medical supplies for emergency obstetric care: experience of health facility managers in a rural District of Tanzania. BMC Pregnancy and Childbirth, 14(1). doi:10.1186/1471-2393-14-108Beck, M. J., Okerblom, D., Kumar, A., Bandyopadhyay, S., & Scalzi, L. V. (2016). Lean intervention improves patient discharge times, improves emergency department throughput and reduces congestion. Hospital Practice, 44(5), 252-259. doi:10.1080/21548331.2016.1254559Morais Oliveira, M., Marti, C., Ramlawi, M., Sarasin, F. P., Grosgurin, O., Poletti, P.-A., … Rutschmann, O. T. (2018). Impact of a patient-flow physician coordinator on waiting times and length of stay in an emergency department: A before-after cohort study. PLOS ONE, 13(12), e0209035. doi:10.1371/journal.pone.0209035Vermeulen, M. J., Stukel, T. A., Boozary, A. S., Guttmann, A., & Schull, M. J. (2016). The Effect of Pay for Performance in the Emergency Department on Patient Waiting Times and Quality of Care in Ontario, Canada: A Difference-in-Differences Analysis. Annals of Emergency Medicine, 67(4), 496-505.e7. doi:10.1016/j.annemergmed.2015.06.028Singh, S., Lin, Y.-L., Nattinger, A. B., Kuo, Y.-F., & Goodwin, J. S. (2015). Variation in readmission rates by emergency departments and emergency department providers caring for patients after discharge. Journal of Hospital Medicine, 10(11), 705-710. doi:10.1002/jhm.2407Källberg, A.-S., Göransson, K. E., Florin, J., Östergren, J., Brixey, J. J., & Ehrenberg, A. (2015). Contributing factors to errors in Swedish emergency departments. International Emergency Nursing, 23(2), 156-161. doi:10.1016/j.ienj.2014.10.002Riga, M., Vozikis, A., Pollalis, Y., & Souliotis, K. (2015). MERIS (Medical Error Reporting Information System) as an innovative patient safety intervention: A health policy perspective. 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A., Yang, J., Altieri, M., Patterson, W., Peoples, B., Chen, H., … Pryor, A. D. (2016). Rates and Risk Factors for Unplanned Emergency Department Utilization and Hospital Readmission Following Bariatric Surgery. Annals of Surgery, 263(5), 956-960. doi:10.1097/sla.0000000000001536Rigobello, M. C. G., Carvalho, R. E. F. L. de, Guerreiro, J. M., Motta, A. P. G., Atila, E., & Gimenes, F. R. E. (2017). The perception of the patient safety climate by professionals of the emergency department. International Emergency Nursing, 33, 1-6. doi:10.1016/j.ienj.2017.03.003Farmer, B. (2016). Patient Safety in the Emergency Department. Emergency Medicine, 48(9), 396-404. doi:10.12788/emed.2016.0052Liu, H.-C., You, J.-X., Zhen, L., & Fan, X.-J. (2014). A novel hybrid multiple criteria decision making model for material selection with target-based criteria. Materials & Design, 60, 380-390. doi:10.1016/j.matdes.2014.03.071Kou, G., Ergu, D., & Shang, J. (2014). Enhancing data consistency in decision matrix: Adapting Hadamard model to mitigate judgment contradiction. European Journal of Operational Research, 236(1), 261-271. doi:10.1016/j.ejor.2013.11.035Keshavarz Ghorabaee, M., Amiri, M., Zavadskas, E. K., & Antucheviciene, J. (2017). Supplier evaluation and selection in fuzzy environments: a review of MADM approaches. Economic Research-Ekonomska Istraživanja, 30(1), 1073-1118. doi:10.1080/1331677x.2017.1314828Barrios, M. A. O., De Felice, F., Negrete, K. P., Romero, B. A., Arenas, A. Y., & Petrillo, A. (2016). An AHP-Topsis Integrated Model for Selecting the Most Appropriate Tomography Equipment. International Journal of Information Technology & Decision Making, 15(04), 861-885. doi:10.1142/s021962201640006xYeh, D.-Y., & Cheng, C.-H. (2016). Performance Management of Taiwan’s National Hospitals. International Journal of Information Technology & Decision Making, 15(01), 187-213. doi:10.1142/s0219622014500199Chen, T.-Y. (2014). An Interactive Signed Distance Approach for Multiple Criteria Group Decision-Making Based on Simple Additive Weighting Method with Incomplete Preference Information Defined by Interval Type-2 Fuzzy Sets. International Journal of Information Technology & Decision Making, 13(05), 979-1012. doi:10.1142/s0219622014500229Gou, X., Xu, Z., & Liao, H. (2019). Hesitant Fuzzy Linguistic Possibility Degree-Based Linear Assignment Method for Multiple Criteria Decision-Making. International Journal of Information Technology & Decision Making, 18(01), 35-63. doi:10.1142/s0219622017500377Saksrisathaporn, K., Bouras, A., Reeveerakul, N., & Charles, A. (2016). Application of a Decision Model by Using an Integration of AHP and TOPSIS Approaches within Humanitarian Operation Life Cycle. International Journal of Information Technology & Decision Making, 15(04), 887-918. doi:10.1142/s0219622015500261Hsiao, B., & Chen, L.-H. (2019). 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Assessing Recent Smoking Status by Measuring Exhaled Carbon Monoxide Levels

The main expectations of applying proteomics technologies to clinical questions are the discovery of disease related biomarkers. Despite technological advancement to increase proteome coverage and depth to meet these expectations the number of generated biomarkers for clinical use is small. One of the reasons is that found potential biomarkers often are false discoveries. Small sample sizes, in combination with patient sample heterogeneity increase the risk of false discoveries. To be able to extract relevant biological information from such data, high demands are put on the experimental design and the use of sensitive and quantitatively accurate technologies. The overall aim of this thesis was to apply quantitative proteomics methods for biomarker discovery in clinical samples. A method for reducing bias by controlling for individual variation in smoking habits is described in paper I. The aim of the method was objective assessment of recent smoking in clinical studies on inflammatory responses. In paper II, the proteome of alveolar macrophages obtained from smoking subjects with and without the inflammatory lung disease chronic obstructive pulmonary disease (COPD) were quantified by two-dimensional gel-electrophoresis (2-DE). A gender focused analysis showed protein level differences within the female group, with down-regulation of lysosomal pathway and up-regulation of oxidative pathway in COPD patients. Paper III, a mass spectrometry based proteomics analysis of tumour samples, contributes to the molecular understanding of vulvar squamous cell carcinoma (VSCC) and we identified a high risk patient subgroup of HPV-negative tumours based on the expression of four proteins, further suggesting that this subgroup is characterized by an altered ubiquitin-proteasome signalling pathway. Paper III describes a data analysis workflow for the extraction of biological information from quantitative mass spectrometry based proteomics data. High patient-to-patient tumour proteome variability was addressed by using pathway profiling on individual tumour data, followed by comparison of pathway association ranks in a multivariate analysis. We show that pathway data on individual tumour level can detect subpopulations of patients and identify pathways of specific importance in pre-defined clinical groups by the use of multivariate statistics. In paper IV, the potentials and limits of quantitative mass spectrometry on clinical samples was evaluated by defining the quantitative accuracy of isobaric labels and label-free quantification. Quantification by isobaric labels in combination with pI pre-fractionation showed a lower limit of quantification (LOQ) than a label-free analysis without pI pre-fractionation, and 6-plex TMT were more sensitive than 8-plex iTRAQ. Precursor mixing measured by isolation interference (MS1 interference) is more linked to the quantitative accuracy of isobaric labels than reporter ion interference (MS2 interference). Based on that we could define recommendations for how much isolation interference that can be accepted; in our data <30% isolation interference had little effect the quantitative accuracy. In conclusion, getting biological knowledge from proteomics studies requires a careful study design, control of possible confounding factors and the use of clinical data to identify disease subtypes. Further, to be able to draw conclusions from the data, the analysis requires accurate quantitative data and robust statistical tools to detect significant protein alterations. Methods around these issues are developed and discussed in this thesis

Tissue Harvester with Functional Valve (THFV): Shidham's device for reproducibly higher specimen yield by fine needle aspiration biopsy with easy to perform steps

BACKGROUND: Fine needle aspiration biopsy (FNAB) cytology has been a highly effective methodology for tissue diagnosis and for various ancillary studies including molecular tests. In addition to other benefits, FNAB predominantly retrieves the diagnostic loosely cohesive cells in the lesion as compared to the adjacent supporting stroma with relatively higher cohesiveness. However, FNAB procedure performed with currently available resources is highly skill dependent with inter-performer variability, which compromises its full potential as a diagnostic tool. In this study we report a device overcoming these limitations. METHODS: 'Tissue Harvester with Functional Valve' (THFV) was evaluated as part of a phase 1 National Institute of Health (NIH) research grant under Small Business Technology Transfer (STTR) Program. Working prototypes of the device were prepared. Each of the four cytopathologists with previous cytopathology fellowship training and experience in performing FNAB evaluated 5 THFV and 5 hypodermic needles resulting in 40 specimens (20 with THFV, 20 with hypodermic needles). A piece of fresh cattle liver stuffed in latex glove was used as the specimen. Based on these results a finished design was finalized. RESULTS: The smears and cell blocks prepared from the specimens obtained by THFV were superior in terms of cellularity to specimens obtained with hypodermic needles. The tissuecrit of specimens obtained with THFV ranged from 70 to 100 μl (mean 87, SD 10), compared to 17 to 30 μl (mean 24, SD 4) with conventional hypodermic needles (p < .0001, Student t-test). The technical ease [on a scale of 1 (easy) to 5 (difficult)] with THFV ranged from 1 to 2 as compared to 2 to 3 with hypodermic needles. CONCLUSION: The specimen yield with the new THFV was significantly higher when compared to hypodermic needles. Also, the FNAB procedure with THFV was relatively easier in comparison with hypodermic needles. The final version of Shidham's THFV device would improve the FNAB specimen yield by eliminating the skill factor. The increased specimen yield by this device would also facilitate wider application of FNAB specimens for various ancillary tests, including molecular tests