82 results on '"B. Taner"'
Search Results
2. Comparison of machine-learning techniques for landslide susceptibility mapping using two-level random sampling (2LRS) in Alakir catchment area, Antalya, Turkey
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Ada, Metehan and San, B. Taner
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- 2017
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3. Tackling Biased Baselines in the Risk-Sensitive Evaluation of Retrieval Systems
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Dinçer, B. Taner, Ounis, Iadh, Macdonald, Craig, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, de Rijke, Maarten, editor, Kenter, Tom, editor, de Vries, Arjen P., editor, Zhai, ChengXiang, editor, de Jong, Franciska, editor, Radinsky, Kira, editor, and Hofmann, Katja, editor
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- 2014
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4. An evaluation of SVM using polygon-based random sampling in landslide susceptibility mapping: The Candir catchment area (western Antalya, Turkey)
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San, B. Taner
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- 2014
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5. Sentence Boundary Detection in Turkish
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Dinçer, B. Taner, Karaoğlan, Bahar, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, and Yakhno, Tatyana, editor
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- 2005
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6. he Effect of Part-of-Speech Tagging on IR Performance for Turkish
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Dinçer, B. Taner, Karaoğlan, Bahar, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Aykanat, Cevdet, editor, Dayar, Tuǧrul, editor, and Körpeoğlu, İbrahim, editor
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- 2004
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7. Stemming in Agglutinative Languages: A Probabilistic Stemmer for Turkish
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Dinçer, B. Taner, Karaoğlan, Bahar, Goos, Gerhard, editor, Hartmanis, Juris, editor, van Leeuwen, Jan, editor, Yazıcı, Adnan, editor, and Şener, Cevat, editor
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- 2003
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8. An assessment on the use of Terra ASTER L3A data in landslide susceptibility mapping.
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Hakan Ahmet Nefeslioglu, B. Taner San, Candan Gokceoglu, and T. Y. Duman
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- 2012
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9. Clinical outcomes of hepatitis C treatment before and after kidney transplantation and its impact on time to transplant: A multicenter study
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Hugo E. Vargas, Eduardo A. Rodriguez, C. B. Taner, Amy E. Chervenak, Surakit Pungpapong, Maxwell L. Smith, Bashar Aqel, Kristen Ryland, S. Nidamanuri, Nan Zhang, Kunam S. Reddy, Janna L. Huskey, Omar Y. Mousa, Andrew P. Keaveny, Diana L. Franco, and David M. Chascsa
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Transplantation ,medicine.medical_specialty ,Cirrhosis ,business.industry ,Hepatitis C ,030230 surgery ,medicine.disease ,03 medical and health sciences ,Liver disease ,surgical procedures, operative ,0302 clinical medicine ,Tolerability ,Interquartile range ,Internal medicine ,medicine ,Immunology and Allergy ,030211 gastroenterology & hepatology ,Pharmacology (medical) ,business ,Kidney transplantation ,Kidney disease - Abstract
Waitlist time for kidney transplantation is long but may be shortened with the utilization of hepatitis C positive allografts. We retrospectively reviewed the course of 36 hepatitis C positive patients awaiting kidney transplantation at 2 large centers within the same health system, with near-identical care delivery models with the exception of timing of hepatitis C treatment, to determine the impact of timing of hepatitis C treatment on access to transplant, waitlist time, and treatment efficacy and tolerability. The majority of patients had hepatitis C genotype 1a or 1b, and all received direct acting antiviral therapy with 100% treatment response. One patient underwent transplantation in the pretransplant treatment group. The 1-year transplantation rate was 12.5% vs 67.9% (P = .0013) in those treated posttransplantation. The median waitlist time in the posttransplant group was 122 (interquartile range [IQR] 21.5, 531.0) days, which was significantly shorter than the center's regional and national wait time. Pathologic review revealed no difference in allograft quality. Overall treatment related adverse events were not different between the 2 groups. A strategy of posttransplant hepatitis C treatment increased access to transplant and reduced waitlist time. Delaying treatment until after transplant did not appear to adversely affect recipients' kidney allograft or overall survival.
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- 2018
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10. Noneligible Donors as a Strategy to Decrease the Organ Shortage
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Kristopher P. Croome, C. B. Taner, David D. Lee, and Andrew P. Keaveny
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Male ,Organ procurement organization ,United Network for Organ Sharing ,Brain Death ,medicine.medical_specialty ,Tissue and Organ Procurement ,Economic shortage ,030230 surgery ,03 medical and health sciences ,Match model ,Liver disease ,0302 clinical medicine ,Risk Factors ,Internal medicine ,medicine ,Humans ,Immunology and Allergy ,Pharmacology (medical) ,Aged ,Transplantation ,business.industry ,Graft Survival ,Organ Transplantation ,Prognosis ,medicine.disease ,Tissue Donors ,Donation after brain death ,Surgery ,Death ,Survival Rate ,Organ procurement ,Liver donors ,Female ,030211 gastroenterology & hepatology ,business ,Follow-Up Studies - Abstract
Organ procurement organization (OPO) performance is generally evaluated by the number of organ procurement procedures divided by the number of eligible deaths (donation after brain death [DBD] donors aged70 years), whereas the number of noneligible deaths (including donation after cardiac death donors and DBD donors aged70 years) is not tracked. The present study aimed to investigate the variability in the proportion of noneligible liver donors by the 58 donor service areas (DSAs). Patients undergoing liver transplant (LT) between 2011 and 2015 were obtained from the United Network for Organ Sharing Standard Transplant Analysis and Research file. LTs from noneligible and eligible donors were compared. The proportion of noneligible liver donors by DSA varied significantly, ranging from 0% to 19.6% of total liver grafts used. In transplant programs, the proportion of noneligible liver donors used ranged from 0% to 35.3%. On linear regression there was no correlation between match Model for End-Stage Liver Disease score for programs in a given DSA and proportion of noneligible donors used from the corresponding DSA (p = 0.14). Noneligible donors remain an underutilized resource in many OPOs. Policy changes to begin tracking noneligible donors and learning from OPOs that have high noneligible donor usage are potential strategies to increase awareness and pursuit of these organs.
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- 2017
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11. Sentence Boundary Detection in Turkish
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Dinçer, B. Taner, primary and Karaoğlan, Bahar, additional
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- 2004
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12. Stemming in Agglutinative Languages: A Probabilistic Stemmer for Turkish
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Dinçer, B. Taner, primary and Karaoğlan, Bahar, additional
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- 2003
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13. A computational morphological lexicon for Turkish: TrLex
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Ozkan Aslan, Serkan Gunal, B. Taner Dinçer, Anadolu Üniversitesi, Mühendislik Fakültesi, Bilgisayar Mühendisliği Bölümü, and Günal, Serkan
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Agglutinative language ,Morphology ,Linguistics and Language ,Computer science ,Turkish ,Compounding ,02 engineering and technology ,computer.software_genre ,Lexicon ,Language and Linguistics ,Field (computer science) ,Morphological Lexicon ,0202 electrical engineering, electronic engineering, information engineering ,Lexical Markup Framework ,060201 languages & linguistics ,business.industry ,06 humanities and the arts ,Word formation ,Part of speech ,language.human_language ,0602 languages and literature ,Morphological analysis ,language ,020201 artificial intelligence & image processing ,Artificial intelligence ,Derivation ,business ,computer ,Natural language processing - Abstract
WOS: 000430906100002, A morphological lexicon that is a computational source should be considered together with derivational morphology especially for agglutinative languages. To the best of our knowledge, in the Turkish language there has been no study that analyzes the derivational suffixes on the lexicon in a computational paradigm. This study provides a very rich lexical resource, filling a gap in the field, and would hopefully lead to new related studies as well. The morphological lexicon can be used in morphological analysis as well as in several other tasks, such as stemming and part of speech (POS) tagging. In this study, we introduce a morphological lexicon named TrLex and present its components, preparation processes and some statistics. We observed that more than half of the single-word lemmas (56.7%) are in the derived structure. Since the word formation in Turkish prefer the morphological processes, this number is higher than the rate of compound-type words (2.7%). As a result of the work, we obtained a knowledge-intensive data table including several fields such as form, structure, semantic information. We also extracted Lexical Markup Framework (LMF) formatted file containing only morphological and POS information and made the file freely available, Anadolu University [1410F415], This work was supported by Anadolu University, Fund of Scientific Research Projects [grant number 1410F415].
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- 2018
14. Simultaneous Liver Kidney Transplant (SLK) Allocation Policy Change Proposal: Is It Really a Smart Move?
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Thomas A. Gonwa, Hani M. Wadei, and C. B. Taner
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Transplantation ,medicine.medical_specialty ,Kidney ,Cirrhosis ,business.industry ,medicine.medical_treatment ,030230 surgery ,Liver transplantation ,medicine.disease ,Kidney Transplantation ,Liver Transplantation ,03 medical and health sciences ,0302 clinical medicine ,medicine.anatomical_structure ,Clinical decision making ,Liver ,medicine ,Simultaneous liver kidney ,Immunology and Allergy ,030211 gastroenterology & hepatology ,Pharmacology (medical) ,Intensive care medicine ,business ,Kidney transplantation - Published
- 2016
15. Clathrin promotes centrosome integrity in early mitosis through stabilization of centrosomal ch-TOG
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Sabrina B. Taner, Sophia R. Majeed, Ivan R. Corrêa, Stéphane M. Camus, Frances M. Brodsky, Timothy Evans, Stephen J. Doxsey, Chih-Ying Chen, and Amy B. Foraker
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RNA Stability ,Aurora A kinase ,Mitosis ,Clathrin ,Clathrin Heavy Chains ,03 medical and health sciences ,0302 clinical medicine ,Humans ,RNA, Small Interfering ,Metaphase ,030304 developmental biology ,Centrosome ,0303 health sciences ,biology ,Cell Biology ,Clathrin Light Chains ,Cell biology ,biology.protein ,RNA Interference ,Microtubule-Associated Proteins ,Multipolar spindles ,030217 neurology & neurosurgery ,HeLa Cells - Abstract
Clathrin depletion by ribonucleic acid interference (RNAi) impairs mitotic spindle stability and cytokinesis. Depletion of several clathrin-associated proteins affects centrosome integrity, suggesting a further cell cycle function for clathrin. In this paper, we report that RNAi depletion of CHC17 (clathrin heavy chain 17) clathrin, but not the CHC22 clathrin isoform, induced centrosome amplification and multipolar spindles. To stage clathrin function within the cell cycle, a cell line expressing SNAP-tagged clathrin light chains was generated. Acute clathrin inactivation by chemical dimerization of the SNAP-tag during S phase caused reduction of both clathrin and ch-TOG (colonic, hepatic tumor overexpressed gene) at metaphase centrosomes, which became fragmented. This was phenocopied by treatment with Aurora A kinase inhibitor, suggesting a centrosomal role for the Aurora A–dependent complex of clathrin, ch-TOG, and TACC3 (transforming acidic coiled-coil protein 3). Clathrin inactivation in S phase also reduced total cellular levels of ch-TOG by metaphase. Live-cell imaging showed dynamic clathrin recruitment during centrosome maturation. Therefore, we propose that clathrin promotes centrosome maturation by stabilizing the microtubule-binding protein ch-TOG, defining a novel role for the clathrin–ch-TOG–TACC3 complex.
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- 2012
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16. Evaluation of cross-track illumination in EO-1 Hyperion imagery for lithological mapping
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M. Lutfi Suzen and B. Taner San
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Wavelength ,General Earth and Planetary Sciences ,Hyperspectral imaging ,Stage (hydrology) ,Atmospheric column ,Geologic map ,Geology ,Shortwave infrared ,Vegetation cover ,VNIR ,Remote sensing - Abstract
Hyperspectral remote sensing data is a powerful tool for discriminating lithological units and for the preparation of mineral maps for alteration studies. The spaceborne hyperspectral Hyperion sensor, despite its narrow swath width ∼7.5 km, possesses great potential with its 196 channels within the wavelength range 426.82–2395.50 nm. Although it has many advantages such as low cost and on-demand coverage, much uncertainty exists in the utility of its applications. For example, poor signal-to-noise ratio, the presence of sensor-specific defects and thicker atmospheric column due to its spaceborne platform makes certain environmental and geological applications difficult or impossible. In this article we demonstrate these calibration-related uncertainties, which are manifest from the preprocessing stage to the classification stage. In addition, the intimate mixing of minerals within specific targets, for example within individual outcropping lithological units or endmembers, adds uncertainty to our spectral discrimination results. The aim of this study was to develop and evaluate an approach for geological mapping of outcrops with Earth Observing-1 EO-1 Hyperion data. Atmospheric corrections and correction for cross-track illumination CTI variations smile were determined at different wavelength regions: the visible–near-infrared VNIR; 420–1000 nm and shortwave infrared SWIR; 1000–2400 nm regions. Our methodology was tested in a selected site at Central Anatolia, Turkey containing minimal vegetation cover. The results obtained from the image analyses were then compared and assessed with field observations and spectral measurements.
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- 2011
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17. Risk-Sensitive Evaluation And Learning To Rank Using Multiple Baselines
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B. Taner Dinçer, Craig Macdonald, and Iadh Ounis
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Computer science ,business.industry ,02 engineering and technology ,Risk sensitive ,computer.software_genre ,User experience design ,Ranking ,Robustness (computer science) ,020204 information systems ,0202 electrical engineering, electronic engineering, information engineering ,020201 artificial intelligence & image processing ,Learning to rank ,Data mining ,Baseline (configuration management) ,business ,computer ,Statistic - Abstract
A robust retrieval system ensures that user experience is\ud not damaged by the presence of poorly-performing queries.\ud Such robustness can be measured by risk-sensitive evaluation\ud measures, which assess the extent to which a system\ud performs worse than a given baseline system. However, using\ud a particular, single system as the baseline suffers from\ud the fact that retrieval performance highly varies among IR\ud systems across topics. Thus, a single system would in general\ud fail in providing enough information about the real baseline\ud performance for every topic under consideration, and\ud hence it would in general fail in measuring the real risk associated\ud with any given system. Based upon the Chi-squared\ud statistic, we propose a new measure ZRisk that exhibits more\ud promise since it takes into account multiple baselines when\ud measuring risk, and a derivative measure called GeoRisk,\ud which enhances ZRisk by also taking into account the overall\ud magnitude of effectiveness. This paper demonstrates\ud the benefits of ZRisk and GeoRisk upon TREC data, and\ud how to exploit GeoRisk for risk-sensitive learning to rank,\ud thereby making use of multiple baselines within the learning\ud objective function to obtain effective yet risk-averse/robust\ud ranking systems. Experiments using 10,000 topics from the\ud MSLR learning to rank dataset demonstrate the efficacy of\ud the proposed Chi-square statistic-based objective function.
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- 2016
18. Postoperative hematoma following inguinal herniorrhaphy: patient characteristics leading to increased risk
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Susan M. Greenlee, David R. Farley, Gustavo S. Oderich, E. B. Cragun, C. B. Taner, Dirk R. Larson, and Rory L. Smoot
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Adult ,Male ,medicine.medical_specialty ,Minnesota ,medicine.medical_treatment ,Postoperative hematoma ,Hernia, Inguinal ,Groin ,Postoperative Complications ,Hematoma ,Risk Factors ,medicine ,Humans ,Hernia ,Aged ,Proportional Hazards Models ,Retrospective Studies ,Aged, 80 and over ,Univariate analysis ,Chi-Square Distribution ,business.industry ,Hazard ratio ,Anticoagulants ,Middle Aged ,Surgical Mesh ,medicine.disease ,Hernia repair ,Surgery ,Inguinal hernia ,Logistic Models ,medicine.anatomical_structure ,Case-Control Studies ,Anesthesia ,Female ,Warfarin ,business - Abstract
Although relatively infrequent, groin hematoma following inguinal herniorrhaphy is a morbid complication with major ramifications of mesh infection and hernia recurrence. We have sensed an increasing frequency of this complication in our tertiary referral practice and sought to determine whether or not significant risk factors could be identified. In this matched case–control study (1995–2003), we identified 53 patients with groin hematomas and paired them with 106 age- and gender-matched controls. Patient and procedure characteristics were analyzed using chi-square and both univariate and multivariable, conditional logistic regression analysis. The 53 patients developing groin hematoma following inguinal hernia repair (mean age = 65, range 22–87, 90% male) were well matched with 106 controls (mean age = 65, range 22–87, 90% male). There was no significant difference in the location (left, right, bilateral), type (direct, indirect, pantaloon, first repair, or recurrent), or technique of hernia repair (Bassini, Lichtenstein, mesh plug, endoscopic, or McVay) between groups. While univariate analysis identified Coumadin usage (P
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- 2007
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19. Transferring Learning To Rank Models for Web Search
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Craig Macdonald, B. Taner Dinçer, and Iadh Ounis
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Information retrieval ,Computer science ,business.industry ,Best practice ,InformationSystems_INFORMATIONSTORAGEANDRETRIEVAL ,Transferability ,computer.software_genre ,Feature (machine learning) ,Learning to rank ,Artificial intelligence ,business ,Null hypothesis ,computer ,Natural language processing - Abstract
Learning to rank techniques provide mechanisms for combining document feature values into learned models that produce effective rankings. However, issues concerning the transferability of learned models between different corpora or subsets of the same corpus are not yet well understood. For instance, is the importance of different feature sets consistent between subsets of a corpus, or whether a learned model obtained on a small subset of the corpus effectively transfer to the larger corpus? By formulating our experiments around two null hypotheses, in this work, we apply a full-factorial experiment design to empirically investigate these questions using the ClueWeb09 and ClueWeb12 corpora, combined with queries from the TREC Web track. Among other observations, our experiments reveal that Clue-Web09 remains an effective choice of training corpus for learning effective models for ClueWeb12, and also that the importance of query independent features varies among the ClueWeb09 and ClueWeb12 corpora. In doing so, this work contributes an important study into the transferability of learning to rank models, as well as empirically-derived best practices for effective retrieval on the ClueWeb12 corpus.
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- 2015
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20. Early Allograft Dysfunction After Liver Transplantation Is Associated With Short- and Long-Term Kidney Function Impairment
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E. Golan, C. B. Taner, Martin L. Mai, Andrew P. Keaveny, David D. Lee, R. Brotman, Hani M. Wadei, and Kristopher P. Croome
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Graft Rejection ,Male ,medicine.medical_specialty ,medicine.medical_treatment ,Urology ,Renal function ,030230 surgery ,Liver transplantation ,urologic and male genital diseases ,Kidney Function Tests ,03 medical and health sciences ,0302 clinical medicine ,Postoperative Complications ,Risk Factors ,medicine ,Immunology and Allergy ,Humans ,Pharmacology (medical) ,Renal replacement therapy ,Risk factor ,Transplantation ,business.industry ,Liver Diseases ,Organ dysfunction ,Graft Survival ,Acute kidney injury ,Odds ratio ,Acute Kidney Injury ,Middle Aged ,medicine.disease ,Allografts ,Prognosis ,female genital diseases and pregnancy complications ,Tissue Donors ,Surgery ,Liver Transplantation ,Survival Rate ,Kidney Failure, Chronic ,030211 gastroenterology & hepatology ,Female ,medicine.symptom ,Primary Graft Dysfunction ,business ,Kidney disease ,Follow-Up Studies ,Glomerular Filtration Rate - Abstract
Early allograft dysfunction (EAD) after liver transplantation (LT) is related to ischemia-reperfusion injury and may lead to a systemic inflammatory response and extrahepatic organ dysfunction. We evaluated the effect of EAD on new-onset acute kidney injury (AKI) requiring renal replacement therapy within the first month and end-stage renal disease (ESRD) within the first year post-LT in 1325 primary LT recipients. EAD developed in 358 (27%) of recipients. Seventy-one (5.6%) recipients developed AKI and 38 (2.9%) developed ESRD. Compared with those without EAD, recipients with EAD had a higher risk of AKI and ESRD (4% vs. 9% and 2% vs. 6%, respectively, p < 0.001 for both). Multivariate logistic regression analysis showed an independent relationship between EAD and AKI as well as ESRD (odds ratio 3.5, 95% confidence interval 1.9-6.4, and odds ratio 3.1, 95% confidence interval 11.9-91.2, respectively). Patients who experienced both EAD and AKI had inferior 1-, 3-, 5-, and 10-year patient and graft survival compared with those with either EAD or AKI alone, while those who had neither AKI nor EAD had the best outcomes (p < 0.001). Post-LT EAD is a risk factor for both AKI and ESRD and should be considered a target for future intervention to reduce post-LT short- and long-term renal dysfunction.
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- 2015
21. Antithymocyte Globulin Induction and Rapid Steroid Taper Leads to Excellent Results in Kidney Transplantation With Donation After Cardiac Death Donors: Importance of Rejection and Delayed Graft Function
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W. K. Mai, Thomas A. Gonwa, Martin L. Mai, Hani M. Wadei, C. B. Taner, and M. B. Prendergast
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Graft Rejection ,Male ,medicine.medical_specialty ,medicine.medical_treatment ,Urology ,Delayed Graft Function ,Renal function ,chemistry.chemical_compound ,Biopsy ,medicine ,Humans ,Kidney transplantation ,Aged ,Antilymphocyte Serum ,Transplantation ,Kidney ,Creatinine ,Proteinuria ,medicine.diagnostic_test ,business.industry ,Immunosuppression ,Middle Aged ,medicine.disease ,Kidney Transplantation ,Tissue Donors ,Tacrolimus ,Surgery ,Death ,medicine.anatomical_structure ,chemistry ,Female ,Steroids ,medicine.symptom ,business ,Glomerular Filtration Rate - Abstract
Recipients of primary transplants from donation after cardiac death (DCD) donors (n = 40) performed from January 2005 to December 2009 were retrospectively reviewed and compared with recipients of primary transplants from donation after brain death (DBD) donors (n = 142). Patients received rabbit antithymocyte globulin induction and rapid steroid taper (RST; steroids stopped 5 days after surgery). Maintenance immunosuppression included tacrolimus and mycophenolate mofetil. Protocol kidney biopsies, creatinine (Cr), and measured glomerular filtration rate (mGFR; determined by cold iothalamate or 24-h creatinine clearance) were obtained at 1, 4, 12, and 24 months. Kidney biopsies for cause were conducted for unexplained elevated Cr, decline in mGFR, or new proteinuria. Biopsies were graded for rejection according to the Banff criteria. Graft survival at 3 years was 90.0% for DCD recipients and 86.6% for DBD recipients (P = NS). Rejection of any grade diagnosed on any biopsy through the first 2 years occurred in 18 DCD (45%) and 50 DBD (35%) recipients. Rejection of a grade more than Banff borderline occurred in 12.5% DCD and 12.7% DBD recipients. At 2 years, the mean ± SEM Cr and mGFR for DCD recipients with rejection were 1.8 ± 0.29 mg/dL and 59.2 ± 8.5 mL/min versus 1.3 ± 0.11 mg/dL and 67.0 ± 7.8 ml/min for those without rejection. For DBD recipients with rejection, Cr and mGFR at 2 years were 1.7 ± 0.12 mg/dL and 54.0 ± 4.4 mL/min versus 1.4 ± 0.11 mg/dL and 66.6 ± 3.3 ml/min for those without rejection (P = NS). Comparing DCD to DBD, there was no statistical difference in mean Cr or mGFR outcomes. Regardless of group, grafts with delayed graft function had lower 3-year survival. DCD primary kidney transplant recipients treated with rabbit antithymocyte induction and RST have short-term graft survival and function equivalent to DBD recipients. RST appears to be acceptable immunosuppression for DCD recipients.
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- 2013
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22. Control of Immune Responses by Trafficking Cell Surface Proteins, Vesicles and Lipid Rafts to and from the Immunological Synapse
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Anthony I. Magee, Daniel M. Davis, Sabrina B. Taner, Niina J. Pirinen, Björn Önfelt, and Fiona E. McCann
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T cell ,Cell Biology ,Biology ,Biochemistry ,Natural killer cell ,Immunological synapse ,Cell biology ,medicine.anatomical_structure ,Immune system ,Structural Biology ,Genetics ,medicine ,Antigen-presenting cell ,Cell activation ,Molecular Biology ,Lipid raft ,Intracellular - Abstract
Supramolecular clusters at the immunological synapse provide a mechanism for structuring complex communication networks between cells of the immune system. Regulating intra- and intercellular trafficking of proteins and lipids to and from the immunological synapse provides an additional level of complexity in determining the functional outcome of immune cell interactions. An emergent principle is that molecules requiring tightly regulated cell surface expression, e.g. negative regulators of cell activation or molecules promoting cytotoxicity, are trafficked to the immunological synapse from intracellular secretory as required lysosomes. Many molecules required for the early stages of the intercellular communication are already present at the cell surface, sometimes in lipid rafts, and are rapidly translocated laterally to the intercellular contact. Our understanding of these events critically depends on utilizing appropriate technologies for probing supramolecular recognition in live cells. Thus, we also present here a critical discussion of the technologies used to study lipid rafts and, more broadly, a map of the spatial and temporal dimensions covered by current live cell physical techniques, highlighting where advances are needed to exceed current spatial and temporal boundaries.
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- 2004
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23. Imaging immune surveillance by T cells and NK cells
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Paul M. W. French, Konstantina Eleme, Kumiko Yanagi, Leo M. Carlin, Bruno Vanherberghen, Fiona E. McCann, Daniel M. Davis, Klaus Suhling, and Sabrina B. Taner
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T cell ,Immunology ,Biology ,Natural killer cell ,Immunological synapse ,Cell biology ,medicine.anatomical_structure ,Immune system ,Membrane protein ,medicine ,Immunology and Allergy ,Receptor ,Cytoskeleton ,Lipid raft - Abstract
As T cells and natural killer (NK) cells survey the surface of other cells, cognate receptors and ligands are commonly organized into distinct micrometer-scale domains at the intercellular contact, creating an immune or immunological synapse (IS). We aim to address the still unanswered questions of how this organization of proteins aids immune surveillance and how these domains are biophysically constructed. Molecular mechanisms for the formation of the IS include a role for the cytoskeleton, segregation of proteins according to the size of their extracellular domains, and association of proteins with lipid rafts. Towards understanding the function of the IS, it is instructive to compare and contrast the supramolecular organization of proteins at the inhibitory and activating NK cell IS with that at the activating T cell IS. Finally, it is essential to develop new technologies for probing molecular recognition at cell surfaces. Imaging parameters other than fluorescence intensity, such as the lifetime of the fluorophore's excited state, could be used to report on protein environments.
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- 2002
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24. Hypothesis testing for the risk-sensitive evaluation of retrieval systems
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B. Taner Dinçer, Craig Macdonald, Iadh Ounis, and MÜ
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Measure (data warehouse) ,Descriptive statistics ,business.industry ,Computer science ,Machine learning ,computer.software_genre ,Test (assessment) ,Test statistic ,Student's T Test ,Learning to rank ,Artificial intelligence ,Data mining ,business ,computer ,Student's t-test ,Risk-Sensitive Evaluation ,Statistical hypothesis testing ,t-statistic - Abstract
37th Annual International ACM Special Interest Group on Information Retrieval Conference on Research and Development in Information Retrieval - JUL 06-11, 2014 - Gold Coast, AUSTRALIA Dincer, Bekir Taner/0000-0002-0660-7239; Ounis, Iadh/0000-0003-4701-3223 WOS: 000450717600003 The aim of risk-sensitive evaluation is to measure when a given information retrieval (IR) system does not perform worse than a corresponding baseline system for any topic. This paper argues that risk-sensitive evaluation is akin to the underlying methodology of the Student's t test for matched pairs. Hence, we introduce a risk-reward tradeoff measure T-Risk that generalises the existing U-Risk measure (as used in the TREC 2013 Web track's risk-sensitive task) while being theoretically grounded in statistical hypothesis testing and easily interpretable. In particular, we show that T-Risk is a linear transformation of the t statistic, which is the test statistic used in the Student's t test. This inherent relationship between T-Ri(sk) and the t statistic, turns risk-sensitive evaluation from a descriptive analysis to a fully-fledged inferential analysis. Specifically, we demonstrate using past TREC data, that by using the inferential analysis techniques introduced in this paper, we can (1) decide whether an observed level of risk for an IR system is statistically significant, and thereby infer whether the system exhibits a real risk, and (2) determine the topics that individually lead to a significant level of risk. Indeed, we show that the latter permits a state-of-the-art learning to rank algorithm (Lamb-daMART) to focus on those topics in order to learn effective yet risk-averse ranking systems. ACM Special Interest Grp Informat Retrieval, Baidu, Google, Microsoft Res, Tourism & Events Queensland, eBay, Huawei, Seznam cz, Facebook, IBM, Pivotal, Yahoo, Labs, Yandex, Queensland Univ Technol, RMIT Univ, Univ Melbourne, Univ Otago
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- 2014
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25. Risk-Sensitive Evaluation and Learning to Rank using Multiple Baselines
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Dinçer, B. Taner, primary, Macdonald, Craig, additional, and Ounis, Iadh, additional
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- 2016
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26. Avoiding stay in the intensive care unit after liver transplantation: a score to assign location of care
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Stephen Aniskevich, Dana K. Perry, Timothy S. J. Shine, C. B. Taner, Andrew P. Keaveny, Darrin L. Willingham, Juan M. Canabal, Ilynn G. Bulatao, Bhupendra Rawal, and Michael G. Heckman
- Subjects
Adult ,Male ,Independent group ,medicine.medical_specialty ,Scoring system ,Clinical variables ,Adolescent ,medicine.medical_treatment ,Liver transplantation ,law.invention ,Patient safety ,Young Adult ,law ,Immunology and Allergy ,Medicine ,Humans ,Pharmacology (medical) ,Intensive care medicine ,Aged ,Aged, 80 and over ,Transplantation ,Postanesthesia care ,business.industry ,Area under the curve ,Middle Aged ,Intensive care unit ,Liver Transplantation ,Intensive Care Units ,Female ,business ,Postanesthesia Nursing - Abstract
Select liver transplantation (LT) recipients in our program are transferred from operating room to postanesthesia care unit for recovery and extubation with transfer to the ward, completely eliminating an intensive care unit (ICU) stay. Developing a reliable method to determine patients suitable for fast-tracking would be of practical benefit to centers considering this practice. The aim of this study was to create a fast-tracking probability score that could be used to predict successful assignment of care location after LT. Recipient, donor and operative characteristics were assessed for independent association with successful fast-tracking to create a probability score. Of the 1296 LT recipients who met inclusion criteria, 704 (54.3%) were successfully fast-tracked and 592 (45.7%) were directly admitted to the ICU after LT. Based on nine readily available variables at the time of LT, we created a scoring system that classified patients according to the likelihood of being successfully fast-tracked to the surgical ward, with an area under the curve (AUC) of 0.790 (95% CI: 0.765-0.816). This score was validated in an independent group of 372 LT with similar AUC. We describe a score that can be used to predict successful fast-tracking immediately after LT using readily available clinical variables.
- Published
- 2013
27. Impact of psychosocial comorbidities on outcomes in elderly liver transplant recipients
- Author
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Terry D. Schneekloth, Andrew P. Keaveny, M. Picco, Shehzad K. Niazi, Michael G. Heckman, B. Taner, S. Davis, Adriana R. Vasquez, Teresa A. Rummans, and Sheila G. Jowsey-Gregoire
- Subjects
Psychiatry and Mental health ,Clinical Psychology ,medicine.medical_specialty ,business.industry ,medicine ,Intensive care medicine ,business ,Psychosocial - Published
- 2016
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28. Bile duct stenting in liver transplantation
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Lena, Sibulesky, C B, Taner, Dana K, Perry, Darrin L, Willingham, and Justin H, Nguyen
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Male ,Biliary Tract Surgical Procedures ,Humans ,Female ,Bile Ducts ,Liver Transplantation - Published
- 2012
29. Atlas of ischemic cholangiopathy in donation-after-cardiac-death liver transplants
- Author
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Ilynn G. Bulatao, Ricardo Paz-Fumagalli, B. Taner, J. McKinney, Gregory T. Frey, Kirk J. Giesbrandt, and David M. Sella
- Subjects
medicine.medical_specialty ,Pathology ,business.industry ,medicine ,Radiology, Nuclear Medicine and imaging ,Donation after cardiac death ,Liver transplants ,Cardiology and Cardiovascular Medicine ,business ,Surgery - Published
- 2015
- Full Text
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30. Clathrin phosphorylation is required for actin recruitment at sites of bacterial adhesion and internalization
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Marie Christine Prevost, Sabrina B. Taner, Lavanya Vasudevan, Adeline Mallet, Matteo Bonazzi, Jeremy D. Wilbur, Martin Sachse, Frances M. Brodsky, Anna Sartori, Allison Roberts, Pascale Cossart, USC2020, Inst Natl Rech Agron, Interactions Bactéries-Cellules (UIBC), Institut National de la Recherche Agronomique (INRA)-Institut Pasteur [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), University of California [San Francisco] (UCSF), University of California, Institut Pasteur, Institut National de la Sante et de la Recherche Medicale, Institut National de la Recherche Agronomique, European Research Council [233348], National Institutes of Health [GM038093], California Breast Cancer Research Program [15IB-0035], Pasteur Roux Fellowship, Institut National de la Recherche Agronomique (INRA)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM), University of California [San Francisco] (UC San Francisco), University of California (UC), Microscopie ultrastructurale (plate-forme), Institut Pasteur [Paris] (IP), Microscopie Ultrastructurale (Plate-forme), Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), and European Project: 233348,EC:FP7:ERC,ERC-2008-AdG,MODELIST(2009)
- Subjects
[SDV]Life Sciences [q-bio] ,MESH: Microscopy, Fluorescence ,MYOSIN-VI ,COATED PITS ,environment and public health ,Medical and Health Sciences ,Bacterial Adhesion ,MESH: Tyrosine ,chemistry.chemical_compound ,0302 clinical medicine ,MESH: Listeria ,Myosin ,BINDING ,Receptors ,2.2 Factors relating to the physical environment ,MESH: Clathrin ,HUNTINGTIN-INTERACTING PROTEIN-1 ,Aetiology ,Phosphorylation ,Internalization ,MEDIATED ENDOCYTOSIS ,LISTERIA-MONOCYTOGENES ,MESH: Bacterial Proteins ,Research Articles ,Cells, Cultured ,MESH: Receptors, Cell Surface ,media_common ,0303 health sciences ,Microscopy ,LIGHT-CHAIN ,Cultured ,Coated Pits, Cell-Membrane ,Biological Sciences ,Cell biology ,Interaction with host ,Cell Surface ,Host-Pathogen Interactions ,Clathrin adaptor proteins ,Infection ,MESH: Cells, Cultured ,inorganic chemicals ,Listeria ,1.1 Normal biological development and functioning ,media_common.quotation_subject ,Cells ,Receptors, Cell Surface ,macromolecular substances ,Biology ,MESH: Actins ,Transfection ,Clathrin ,Article ,Fluorescence ,03 medical and health sciences ,Bacterial Proteins ,Underpinning research ,E-CADHERIN ,Humans ,MESH: Bacterial Adhesion ,Actin ,030304 developmental biology ,MESH: Humans ,HIP1-RELATED PROTEIN ,MESH: Phosphorylation ,MESH: Transfection ,MESH: Host-Pathogen Interactions ,Tyrosine phosphorylation ,Cell Biology ,Actins ,enzymes and coenzymes (carbohydrates) ,Microscopy, Fluorescence ,chemistry ,Coated Pits ,Hela Cells ,MESH: HeLa Cells ,MESH: Coated Pits, Cell-Membrane ,biology.protein ,bacteria ,Tyrosine ,HOST-CELLS ,Cell-Membrane ,030217 neurology & neurosurgery ,HeLa Cells ,Developmental Biology - Abstract
Clathrin assembles at bacterial adhesion sites and its phosphorylation is required for actin recruitment during bacterial infection., Bacterial pathogens recruit clathrin upon interaction with host surface receptors during infection. Here, using three different infection models, we observed that host–pathogen interactions induce tyrosine phosphorylation of clathrin heavy chain. This modification was critical for recruitment of actin at bacteria–host adhesion sites during bacterial internalization or pedestal formation. At the bacterial interface, clathrin assembled to form coated pits of conventional size. Because such structures cannot internalize large particles such as bacteria, we propose that during infection, clathrin-coated pits serve as platforms to initiate actin rearrangements at bacteria–host adhesion sites. We then showed that the clathrin–actin interdependency is initiated by Dab2 and depends on the presence of clathrin light chain and its actin-binding partner Hip1R, and that the fully assembled machinery can recruit Myosin VI. Together, our study highlights a physiological role for clathrin heavy chain phosphorylation and reinforces the increasingly recognized function of clathrin in actin cytoskeletal organization in mammalian cells.
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- 2011
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31. Interactions of NK cell receptor KIR3DL1*004 with chaperones and conformation-specific antibody reveal a functional folded state as well as predominant intracellular retention
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Karl-Johan Malmberg, Steven G.E. Marsh, Sabrina B. Taner, Allison Roberts, Frances M. Brodsky, Marcelo J. Pando, Jennifer Schellekens, and Peter Parham
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Intracellular Fluid ,Protein Folding ,Protein Conformation ,Immunology ,Endoplasmic Reticulum ,Ligands ,Article ,Cell Line ,Stress, Physiological ,MHC class I ,Immunology and Allergy ,Humans ,Secretion ,Protein Unfolding ,biology ,Endoplasmic reticulum ,Antibodies, Monoclonal ,Receptors, KIR3DL1 ,Molecular biology ,Allotype ,Cell biology ,Killer Cells, Natural ,Protein Transport ,HLA-B Antigens ,Chaperone (protein) ,biology.protein ,Unfolded protein response ,Calreticulin ,Intracellular ,Molecular Chaperones ,Protein Binding - Abstract
Variable interaction between the Bw4 epitope of HLA-B and the polymorphic KIR3DL1/S1 system of inhibitory and activating NK cell receptors diversifies the development, repertoire formation, and response of human NK cells. KIR3DL1*004, a common KIR3DL1 allotype, in combination with Bw4+ HLA-B, slows progression of HIV infection to AIDS. Analysis in this study of KIR3DL1*004 membrane traffic in NK cells shows this allotype is largely misfolded but stably retained in the endoplasmic reticulum, where it binds to the chaperone calreticulin and does not induce the unfolded protein response. A small fraction of KIR3DL1*004 folds correctly and leaves the endoplasmic reticulum to be expressed on the surface of primary NK and transfected NKL cells, in a form that can be triggered to inhibit NK cell activation and secretion of IFN-γ. Consistent with this small proportion of correctly folded molecules, trace amounts of MHC class I coimmunoprecipitated with KIR3DL1*004. There was no indication of any extensive intracellular interaction between unfolded KIR3DL1*004 and cognate Bw4+ HLA-B. A similarly limited interaction of Bw4 with KIR3DL1*002, when both were expressed by the same cell, was observed despite the efficient folding of KIR3DL1*002 and its abundance on the NK cell surface. Several positions of polymorphism modulate KIR3DL1 abundance at the cell surface, differences that do not necessarily correlate with the potency of allotype function. In this context, our results suggest the possibility that the effect of Bw4+ HLA-B and KIR3DL1*004 in slowing progression to AIDS is mediated by interaction of Bw4+ HLA-B with the small fraction of cell surface KIR3DL1*004.
- Published
- 2010
32. Transferring Learning To Rank Models for Web Search
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Macdonald, Craig, primary, Dinçer, B. Taner, additional, and Ounis, Iadh, additional
- Published
- 2015
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33. Polycystic liver disease and liver transplantation: single-institution experience
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Hani P. Grewal, Christopher B. Hughes, Darrin L. Willingham, Winston R. Hewitt, Justin H. Nguyen, and B. Taner
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Male ,medicine.medical_specialty ,medicine.medical_treatment ,Vena Cava, Inferior ,Liver transplantation ,Inferior vena cava ,Nephrectomy ,Intraoperative Period ,medicine ,Humans ,Intraoperative Complications ,Survival rate ,Aged ,Retrospective Studies ,Transplantation ,business.industry ,Polycystic liver disease ,Liver Diseases ,Graft Survival ,Retrospective cohort study ,Perioperative ,Organ Size ,Middle Aged ,medicine.disease ,Kidney Transplantation ,Surgery ,Liver Transplantation ,Radiography ,Survival Rate ,medicine.vein ,Liver ,lipids (amino acids, peptides, and proteins) ,Female ,business ,Erythrocyte Transfusion ,Liver Failure - Abstract
Adult polycystic liver disease (PLD) can cause massive hepatomegaly leading to pain, caval obstruction, and hemorrhage. Many surgical techniques including aspiration, fenestration, and resection have been used to treat PLD. In addition to substantial morbidity and mortality, conservative surgery may have limited success, and palliation may be temporary. With improved results of liver transplantation, it has become the definitive treatment for PLD. We retrospectively reviewed our experience in patients with PLD between 1998 and 2007. Thirteen patients underwent liver only or liver-kidney transplantation. All surgical procedures were performed with preservation of the recipient inferior vena cava and without venovenous bypass (piggyback technique). Our patients experienced a high rate of perioperative morbidity. However, long-term patient and graft survival were excellent.
- Published
- 2008
34. Buccal and palatal talon cusps with pulp extensions on a supernumerary primary tooth
- Author
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H Cem Gungor, B Taner, E Siraci, and Zafer C. Cehreli
- Subjects
Male ,Dentistry ,Computed tomography ,Tooth crown ,stomatognathic system ,Incisor ,medicine ,Image Processing, Computer-Assisted ,Humans ,Replica Techniques ,Radiology, Nuclear Medicine and imaging ,Supernumerary ,cardiovascular diseases ,Tooth, Deciduous ,Dental Enamel ,General Dentistry ,Dental Pulp ,Orthodontics ,medicine.diagnostic_test ,business.industry ,General Medicine ,medicine.disease ,stomatognathic diseases ,medicine.anatomical_structure ,Otorhinolaryngology ,Morphometric analysis ,Tooth, Supernumerary ,Child, Preschool ,Talon cusp ,Supernumerary primary tooth ,cardiovascular system ,Microscopy, Electron, Scanning ,Pulp (tooth) ,business ,Tomography, X-Ray Computed - Abstract
This paper reports an unusual occurrence of talon cusp on a supernumerary primary incisor, presenting on both labial and palatal sides. The tooth was scheduled for extraction due to its interference with the occlusion. Morphometric analysis of the taloned cusps was performed on digitized replicas of the tooth crown using open-source image analysis toolkit (ImageJ). Further non-destructive investigation of the taloned crown under cone-beam X-ray computed tomography revealed pulpal extensions in both talon cusps.
- Published
- 2006
35. Comparison of machine-learning techniques for landslide susceptibility mapping using two-level random sampling (2LRS) in Alakir catchment area, Antalya, Turkey.
- Author
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Ada, Metehan and San, B. Taner
- Subjects
SUPPORT vector machines ,RANDOM forest algorithms ,LANDSLIDE prediction ,STATISTICAL sampling - Abstract
The aim of this study is to make a comparison of the performances of two machine-learning algorithms that support vector machine (SVM) and random forest (RF) for landslide susceptibility mapping. The study makes use of a sampling strategy called two-level random sampling (2LRS). During landslide susceptibility mapping, training and testing samples must be collected from different landslide seed cells, which are then put through a fully independent sampling using the 2LRS algorithm. This approach requires fewer samples for the improvement of the computation time of both machine-learning classifications. The proposed approach was tested in the Alakir catchment area (Western Antalya, Turkey) which features numerous active deep-seated rotational landslides. In order to compare the performance of the machine-learning algorithms, three random sets were generated for SVM and three random sets generated for 10, 100, 1000 and 10,000-tree size RF. A total of 15 models were generated for comparison, and their spatial performances were performed by the area under the receiver-operating characteristic curves, which ranged between 0.82 and 0.87. The highest and lowest performances were recorded from two models in SVM and two models from the 1000-tree and 10,000-tree sized RF, respectively. These results were confirmed the landslide happened just after producing the susceptibility maps in the field. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
36. Control of immune responses by trafficking cell surface proteins, vesicles and lipid rafts to and from the immunological synapse
- Author
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Sabrina B, Taner, Björn, Onfelt, Niina J, Pirinen, Fiona E, McCann, Anthony I, Magee, and Daniel M, Davis
- Subjects
Killer Cells, Natural ,Protein Transport ,Membrane Microdomains ,T-Lymphocytes ,Cytoplasmic Vesicles ,Animals ,Humans ,Membrane Proteins - Abstract
Supramolecular clusters at the immunological synapse provide a mechanism for structuring complex communication networks between cells of the immune system. Regulating intra- and intercellular trafficking of proteins and lipids to and from the immunological synapse provides an additional level of complexity in determining the functional outcome of immune cell interactions. An emergent principle is that molecules requiring tightly regulated cell surface expression, e.g. negative regulators of cell activation or molecules promoting cytotoxicity, are trafficked to the immunological synapse from intracellular secretory as required lysosomes. Many molecules required for the early stages of the intercellular communication are already present at the cell surface, sometimes in lipid rafts, and are rapidly translocated laterally to the intercellular contact. Our understanding of these events critically depends on utilizing appropriate technologies for probing supramolecular recognition in live cells. Thus, we also present here a critical discussion of the technologies used to study lipid rafts and, more broadly, a map of the spatial and temporal dimensions covered by current live cell physical techniques, highlighting where advances are needed to exceed current spatial and temporal boundaries.
- Published
- 2004
37. Cell surface organization of stress-inducible proteins ULBP and MICA that stimulate human NK cells and T cells via NKG2D
- Author
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Daniel M. Davis, Björn Önfelt, Colin R. Hopkins, Konstantina Eleme, Sabrina B. Taner, N. Jan Chalupny, David Cosman, Fiona E. McCann, Lucy M. Collinson, and Anthony I. Magee
- Subjects
T-Lymphocytes ,Immunology ,GPI-Linked Proteins ,Natural killer cell ,Immunological synapse ,Cell Line ,Cell membrane ,Membrane Microdomains ,fluorescence imaging ,MHC class I ,medicine ,Immunology and Allergy ,Humans ,Receptors, Immunologic ,Lipid raft ,DNA Primers ,lipid rafts ,biology ,Base Sequence ,Cell Membrane ,Histocompatibility Antigens Class I ,Intracellular Signaling Peptides and Proteins ,Brief Definitive Report ,immunological synapse ,Membrane Proteins ,natural killer cell ,NKG2D ,Molecular biology ,Cell biology ,Killer Cells, Natural ,ULBP1 ,stomatognathic diseases ,Microscopy, Electron ,medicine.anatomical_structure ,Membrane protein ,NK Cell Lectin-Like Receptor Subfamily K ,biology.protein ,intercellular communication ,Intercellular Signaling Peptides and Proteins ,Receptors, Natural Killer Cell ,lipids (amino acids, peptides, and proteins) ,Carrier Proteins - Abstract
Cell surface proteins major histocompatibility complex (MHC) class I–related chain A (MICA) and UL16-binding proteins (ULBP) 1, 2, and 3 are up-regulated upon infection or tumor transformation and can activate human natural killer (NK) cells. Patches of cross-linked raft resident ganglioside GM1 colocalized with ULBP1, 2, 3, or MICA, but not CD45. Thus, ULBPs and MICA are expressed in lipid rafts at the cell surface. Western blotting revealed that glycosylphosphatidylinositol (GPI)-anchored ULBP3 but not transmembrane MICA, MHC class I protein, or transferrin receptor, accumulated in detergent-resistant membranes containing GM1. Thus, MICA may have a weaker association with lipid rafts than ULBP3, yet both proteins accumulate at an activating human NK cell immune synapse. Target cell lipid rafts marked by green fluorescent protein–tagged GPI also accumulate with ULBP3 at some synapses. Electron microscopy reveals constitutive clusters of ULBP at the cell surface. Regarding a specific molecular basis for the organization of these proteins, ULBP1, 2, and 3 and MICA are lipid modified. ULBP1, 2, and 3 are GPI anchored, and we demonstrate here that MICA is S-acylated. Finally, expression of a truncated form of MICA that lacks the putative site for S-acylation and the cytoplasmic tail can be expressed at the cell surface, but is unable to activate NK cells.
- Published
- 2004
38. Hypothesis testing for the risk-sensitive evaluation of retrieval systems
- Author
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Dinçer, B. Taner, primary, Macdonald, Craig, additional, and Ounis, Iadh, additional
- Published
- 2014
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39. Ischemic cholangiopathy in donation-after-cardiac-death liver transplants: anatomic findings and predictors of clinical outcomes
- Author
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J. McKinney, David M. Sella, Ricardo Paz-Fumagalli, Kirk J. Giesbrandt, B. Taner, Gregory T. Frey, and Ilynn G. Bulatao
- Subjects
medicine.medical_specialty ,business.industry ,General surgery ,medicine ,Radiology, Nuclear Medicine and imaging ,Donation after cardiac death ,Liver transplants ,Cardiology and Cardiovascular Medicine ,business ,Surgery - Published
- 2015
- Full Text
- View/download PDF
40. Imaging immune surveillance by T cells and NK cells
- Author
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Fiona E, McCann, Klaus, Suhling, Leo M, Carlin, Konstantina, Eleme, Sabrina B, Taner, Kumiko, Yanagi, Bruno, Vanherberghen, Paul M W, French, and Daniel M, Davis
- Subjects
T-Lymphocytes ,Models, Immunological ,Membrane Proteins ,Fluorescence Polarization ,Ligands ,Killer Cells, Natural ,Mice ,Intercellular Junctions ,Membrane Microdomains ,Fluorescence Resonance Energy Transfer ,Animals ,Humans ,Receptors, Immunologic ,Cytoskeleton - Abstract
As T cells and natural killer (NK) cells survey the surface of other cells, cognate receptors and ligands are commonly organized into distinct micrometer-scale domains at the intercellular contact, creating an immune or immunological synapse (IS). We aim to address the still unanswered questions of how this organization of proteins aids immune surveillance and how these domains are biophysically constructed. Molecular mechanisms for the formation of the IS include a role for the cytoskeleton, segregation of proteins according to the size of their extracellular domains, and association of proteins with lipid rafts. Towards understanding the function of the IS, it is instructive to compare and contrast the supramolecular organization of proteins at the inhibitory and activating NK cell IS with that at the activating T cell IS. Finally, it is essential to develop new technologies for probing molecular recognition at cell surfaces. Imaging parameters other than fluorescence intensity, such as the lifetime of the fluorophore's excited state, could be used to report on protein environments.
- Published
- 2002
41. Endothelial function in pigs transgenic for human complement regulating factor
- Author
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Gregor, Warnecke, Sandra R, Severson, Mustafa M, Ugurlu, Cemal B, Taner, John S, Logan, Lisa E, Diamond, Virginia M, Miller, and Christopher G A, McGregor
- Subjects
Male ,Captopril ,Membrane Glycoproteins ,Dose-Response Relationship, Drug ,Endothelin-1 ,Swine ,Natriuretic Peptide, C-Type ,Bradykinin ,Nitric Oxide ,Membrane Cofactor Protein ,Vasodilation ,Antigens, CD ,Animals ,Humans ,Endothelium, Vascular ,Angiotensin I ,Nitric Oxide Synthase ,Calcimycin - Abstract
Expression of human complement regulating factor (hCRF) in porcine organs prevents hyperacute rejection of these organs after xenotransplantation to nonhuman primates. Experiments were designed to characterize endothelial and smooth muscle function of arteries from pigs transgenic for hCD46.Arterial blood from outbred pigs transgenic for hCD46 expression and nontransgenic animals of the same lineage was analyzed for angiotensin-converting enzyme (ACE), C-type natriuretic peptide (CNP), and nitric oxide. Aortic endothelial cells were prepared for measurement of mRNA or activity for nitric oxide synthase (NOS). Rings cut from femoral and pulmonary arteries were suspended in organ chambers for measurement of isometric tension.CNP was significantly greater, ACE was similar, and nitric oxide was significantly less in plasma from transgenic compared with nontransgenic pigs. Neither mRNA nor activity of NOS differed between the groups. Endothelium-dependent relaxations to bradykinin and acetylcholine but not the calcium ionophore were shifted significantly to the left in femoral and pulmonary arteries from hCD46 transgenic pigs compared with nontransgenic pigs. The ACE-inhibitor captopril augmented relaxations similarly in both groups, but NG-monomethyl-L-arginine (L-NMMA) did not inhibit relaxations in rings from transgenic pigs.Data suggest that expression of hCD46 on endothelium of pigs selectively augments endothelium-dependent relaxations to bradykinin by increased release of endothelium-derived factors other than nitric oxide. There does not seem to be any change in activity of ACE or NOS with expression of the human protein. Increased relaxations to bradykinin may be beneficial in lowering vascular resistance when transgenic organs are used for xenotransplantation.
- Published
- 2002
42. Evaluation of cross-track illumination in EO-1 Hyperion imagery for lithological mapping
- Author
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San, B. Taner, primary and Süzen, M. Lütfi, additional
- Published
- 2011
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43. Delayed Graft Function (DGF) Negatively Affects Kidney Function but not Allograft Survival in Donation after Cardiac Death (DCD) Kidney Transplantation
- Author
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Thomas A. Gonwa, Martin L. Mai, L. Sibulesky, W. Farahat, C. B. Taner, M. B. Prendergast, L. Nur, C. Leaphart, and Hani M. Wadei
- Subjects
Transplantation ,medicine.medical_specialty ,business.industry ,Allograft survival ,medicine ,Urology ,Renal function ,Donation after cardiac death ,medicine.disease ,business ,Kidney transplantation ,Delayed Graft Function - Published
- 2012
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44. Antibody Induction with Rapid Steroid Taper Leads to Excellent Results in Kidney Transplant with Donors after Cardiac Death (DCD)
- Author
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Thomas A. Gonwa, Martin L. Mai, Hani M. Wadei, W. K. Mai, M. B. Prendergast, and C. B. Taner
- Subjects
Transplantation ,business.industry ,medicine.medical_treatment ,Antibody induction ,Immunology ,medicine ,business ,Kidney transplant ,Steroid - Published
- 2012
- Full Text
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45. Cyprus Women’s Health Research (COHERE) initiative: determining the relative burden of women’s health conditions and related co-morbidities in an Eastern Mediterranean population
- Author
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M. B. Hocaoglu, S. Gurkas, T. Karaderi, B. Taneri, K. Erguler, B. Barin, E. M. Bilgin, G. Eralp, M. Allison, N. Findikli, K. Boynukalin, M. Bahceci, H. Naci, K. Vincent, S. A. Missmer, C. M. Becker, K. T. Zondervan, and N. Rahmioglu
- Subjects
Benign women’s health conditions ,Prevalence ,Endometriosis ,Uterine fibroids ,PCOS ,Chronic pain conditions ,Gynecology and obstetrics ,RG1-991 ,Public aspects of medicine ,RA1-1270 - Abstract
Abstract Background There is lack of population level data on prevalence and distribution of common benign women’s health conditions such as endometriosis, uterine fibroids, polycystic ovary syndrome from the Eastern Mediterranean region despite their significant consequences on quality of life. In particular, there is complete absence of any health statistics from Northern Cyprus, which is an emerging region in Europe. The Cyprus Women’s Health Research (COHERE) Initiative is the first large-scale cross-sectional study in the region, aiming to determine the relative burden of benign women’s health conditions and related co-morbidities in women living in Northern Cyprus. Methods The COHERE Initiative is a cross-sectional study aiming to recruit 8000 women aged 18–55 years and residing for at least the past 5 years in Northern Cyprus. The study is composed of two main steps: (1) Baseline recruitment, including (i) completion of a detailed health questionnaire, which is an expanded version of the World Endometriosis Research Foundation (WERF) Endometriosis Phenome Harmonisation Project (EPHect) standardised questionnaire, including questions on demographics, menstrual history, hormone use, pregnancy, pain (pelvic pain, bladder and bowel pain, migraine), medical history, family history of illnesses, medication use, life-style factors in relation to a wide range of reproductive and endocrine conditions, resource use (ii) measurement of weight, height, waist/hip circumference and blood pressure, (iii) collection of saliva samples for genotyping. (2) Gynaecology clinic follow up, including a pelvic ultrasound scan (USS). There is also a follow-up food frequency questionnaire (FFQ) targeted to all women taking part in the baseline recruitment with an aim to collect more detailed data on dietary habits. Discussion The COHERE Initiative will generate prevalence rates for conditions, define the clinical profiles for women’s health conditions, and estimate the economic burden of these conditions in Northern Cyprus. The results will also provide insights into the current status of health-care among women living in a currently under-investigated region. The genetic findings will inform future gene mapping studies for investigation of the heritable component of conditions in this population/region. Moreover, the results will be compared with other centres collecting data using EPHect tools globally and will help determine population differences and similarities in disease patterns and clinical profiles. The COHERE Initiative will serve as a resource to conduct hypothesis-driven follow-up studies investigating effect of the ‘Mediterranean life-style’ as well as genetic factors on common benign women’s health conditions that maybe specific to Eastern Mediterranean populations.
- Published
- 2019
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- View/download PDF
46. Synthesis and characterization of new ( E,E )-dioximes and their divalent metal complexes.
- Author
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P. Deveci, E. Özcan, and B. Taner
- Subjects
METAL complexes ,COMPLEX compounds ,NUCLEAR magnetic resonance ,CATIONS - Abstract
Abstract Two new soluble vic-dioxime ligands, 4-isopropylanilineglyoxime (L1H2) and 4-benzylpiperidineglyoxime (L2H2) were prepared by reacting 4-isopropylaniline and 4-benzylpiperidine with anti-chloroglyoxime. Ten metal complexes were obtanied by reacting both ligands with Cu(II),Ni(II),Co(II), Zn(II), and Cd(II) cations. The ligands and their metal complexes were elucidated by elemental analysis, IR, UV-vis, 1H NMR, and 13C NMR and also magnetic moments of the complexes were determined. [ABSTRACT FROM AUTHOR]
- Published
- 2007
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47. Live Cell Linear Dichroism Imaging Reveals Extensive Membrane Ruffling within the Docking Structure of Natural Killer Cell Immune Synapses
- Author
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Daniel Wüstner, Fiona J. Culley, Richard K.P. Benninger, Paul M. W. French, Stephen Young, Tim Schnyder, Daniel M. Davis, Mark A. A. Neil, Björn Önfelt, Sabrina B. Taner, and Bruno Vanherberghen
- Subjects
Membrane ruffling ,Immunological Synapses ,Glycosylphosphatidylinositols ,Cell ,Biophysics ,HLA-C Antigens ,Biology ,Fluorescence ,Natural killer cell ,Immunological synapse ,Cell membrane ,Cell Line, Tumor ,medicine ,Humans ,Cell Line, Transformed ,Microscopy, Confocal ,Biophysical Letter ,Cell Membrane ,Cytoplasmic Vesicles ,Microtubule organizing center ,Cell biology ,Killer Cells, Natural ,medicine.anatomical_structure ,Receptors, KIR2DL1 ,Intracellular ,Algorithms ,Software - Abstract
Udgivelsesdato: 2009-Jan We have applied fluorescence imaging of two-photon linear dichroism to measure the subresolution organization of the cell membrane during formation of the activating (cytolytic) natural killer (NK) cell immune synapse (IS). This approach revealed that the NK cell plasma membrane is convoluted into ruffles at the periphery, but not in the center of a mature cytolytic NK cell IS. Time-lapse imaging showed that the membrane ruffles formed at the initial point of contact between NK cells and target cells and then spread radialy across the intercellular contact as the size of the IS increased, becoming absent from the center of the mature synapse. Understanding the role of such extensive membrane ruffling in the assembly of cytolytic synapses is an intriguing new goal.
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48. Regional Differences and Temporal Changes in the Utilization of HCV-Viremic Donors in Kidney Transplantation.
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Leeaphorn N, Attieh RM, Wadei HM, Mao SA, Mao MA, Pungpapong S, Taner B, Cheungpasitporn W, and Jarmi T
- Subjects
- Humans, United States epidemiology, Hepacivirus, Viremia epidemiology, Kidney Transplantation, Tissue Donors supply & distribution, Hepatitis C epidemiology, Tissue and Organ Procurement statistics & numerical data
- Abstract
Introduction: Despite the data demonstrating an increased utilization of hepatitis C virus (HCV)-viremic kidneys, the acceptance and incorporation of HCV-viremic kidneys are not universal. We aimed to identify regional differences and their temporal changes in the utilization of HCV-viremic kidneys., Methods: Using the Organ Procurement and Transplantation Network database, HCV-viremic kidneys utilized in kidney transplants from March 15, 2019, to March 14, 2023, were included. The utilization of HCV-viremic kidneys across the United States and center-level clustering of HCV-viremic donor kidney transplants into HCV NAT-negative recipients (HCV D+/R- transplants) using Gini coefficients were examined., Results: Significant regional variations were observed, with regions 3, 10, and 11 accounting for 51% of all HCV-viremic kidney utilization. Region 9 benefited the most from HCV-viremic kidney transplants with a high influx of kidney imports from other regions (284.9% gain). Region 8 and region 6 encountered the most substantial losses, with net losses of -44.2% and -41.1%, respectively. HCV D+/R- transplants were concentrated in specific high-volume centers, but trends indicated a gradual increase in a more equitable distribution across centers over time., Conclusions: Significant variations can be observed in the utilization of HCV-viremic kidneys throughout the United States. These variations highlight opportunities for kidney transplant centers in specific regions to adopt policies for HCV-viremic kidney transplants, thereby expanding their donor pool. Encouragingly, an increasing number of kidney transplant centers are adopting HCV D+/R- kidney transplants, indicating positive progress. These trends suggest a more balanced access to HCV-viremic kidneys ahead., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this article., (Copyright © 2024 Elsevier Inc. All rights reserved.)
- Published
- 2024
- Full Text
- View/download PDF
49. Modeling of Cooperative Robotic Systems and Predictive Control Applied to Biped Robots and UAV-UGV Docking with Task Prioritization.
- Author
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Taner B and Subbarao K
- Abstract
This paper studies a cooperative modeling framework to reduce the complexity in deriving the governing dynamical equations of complex systems composed of multiple bodies such as biped robots and unmanned aerial and ground vehicles. The approach also allows for an optimization-based trajectory generation for the complex system. This work also studies a fast-slow model predictive control strategy with task prioritization to perform docking maneuvers on cooperative systems. The method allows agents and a single agent to perform a docking maneuver. In addition, agents give different priorities to a specific subset of shared states. In this way, overall degrees of freedom to achieve the docking task are distributed among various subsets of the task space. The fast-slow model predictive control strategy uses non-linear and linear model predictive control formulations such that docking is handled as a non-linear problem until agents are close enough, where direct transcription is calculated using the Euler discretization method. During this phase, the trajectory generated is tracked with a linear model predictive controller and addresses the close proximity motion to complete docking. The trajectory generation and modeling is demonstrated on a biped robot, and the proposed MPC framework is illustrated in a case study, where a quadcopter docks on a non-holonomic rover using a leader-follower topology.
- Published
- 2024
- Full Text
- View/download PDF
50. Reply to: "Excellent long-term outcomes after sequential hypothermic and normothermic machine perfusion challenges the importance of functional donor warm ischemia time in DCD liver transplantation": Further comments on the changing role of donor warm ischemia time in DCD liver selection in the era of machine perfusion.
- Author
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De Carlis R, Lauterio A, Bernasconi D, and Taner B
- Subjects
- Humans, Warm Ischemia, Liver, Perfusion, Tissue Donors, Organ Preservation, Graft Survival, Liver Transplantation
- Published
- 2023
- Full Text
- View/download PDF
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