26 results on '"Ege, N."'
Search Results
2. Ammonothermal Crystal Growth of Functional Nitrides for Semiconductor Devices: Status and Potential
- Author
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Thomas Wostatek, V. Y. M. Rajesh Chirala, Nathan Stoddard, Ege N. Civas, Siddha Pimputkar, and Saskia Schimmel
- Subjects
ammonothermal ,synthesis ,nitrides ,semiconductors ,solubility ,in situ monitoring ,Technology ,Electrical engineering. Electronics. Nuclear engineering ,TK1-9971 ,Engineering (General). Civil engineering (General) ,TA1-2040 ,Microscopy ,QH201-278.5 ,Descriptive and experimental mechanics ,QC120-168.85 - Abstract
The state-of-the-art ammonothermal method for the growth of nitrides is reviewed here, with an emphasis on binary and ternary nitrides beyond GaN. A wide range of relevant aspects are covered, from fundamental autoclave technology, to reactivity and solubility of elements, to synthesized crystalline nitride materials and their properties. Initially, the potential of emerging and novel nitrides is discussed, motivating their synthesis in single crystal form. This is followed by a summary of our current understanding of the reactivity/solubility of species and the state-of-the-art single crystal synthesis for GaN, AlN, AlGaN, BN, InN, and, more generally, ternary and higher order nitrides. Investigation of the synthesized materials is presented, with a focus on point defects (impurities, native defects including hydrogenated vacancies) based on GaN and potential pathways for their mitigation or circumvention for achieving a wide range of controllable functional and structural material properties. Lastly, recent developments in autoclave technology are reviewed, based on GaN, with a focus on advances in development of in situ technologies, including in situ temperature measurements, optical absorption via UV/Vis spectroscopy, imaging of the solution and crystals via optical (visible, X-ray), along with use of X-ray computed tomography and diffraction. While time intensive to develop, these technologies are now capable of offering unprecedented insight into the autoclave and, hence, facilitating the rapid exploration of novel nitride synthesis using the ammonothermal method.
- Published
- 2024
- Full Text
- View/download PDF
3. The regulation and function of YAP1
- Author
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Ege, N. M. and Sahai, E.
- Subjects
572 - Abstract
Yes-associated protein 1 (YAP1) is a transcriptional regulator that was first described as part of the Hippo signalling cascade. In the last five years, several others regulators have been identified, placing YAP1 at the centre of a much more complex network. One common feature of these different regulatory mechanisms is that YAP1 localises either in the nucleus bound to transcription factors promoting the expression of target genes or in the cytoplasm sequestered into diverse complexes. In vivo studies reveal that YAP1 can promote tumour initiation, progression and metastasis by controlling proliferation and survival of cancer cells. In addition to cancer cells, tumours contain many other cell types such as cancer-associated fibroblasts (CAFs). These cells show a high ability to promote invasion of cancer cells by remodelling the extra-cellular matrix. One possible origin for CAFs is through the local conversion of resident NFs, however the mechanism of this conversion is not fully understood. This thesis aims to understand the function and regulation of YAP1 in fibroblasts during normal development and tumour progression. Analyses of gene expression showed that YAP1 transcriptional activity was upregulated in CAFs compared to NFs. Treatment with actomyosin inhibitors revealed that this upregulation was dependent on the actomyosin cytoskeleton network suggesting a role for mechanotransduction in YAP1 regulation. This high transcriptional activity was associated with a nuclear translocation of YAP1 in CAFs compared to NFs. In order to determine the dynamics of the protein sub-cellular localisation, YAP1 was fused to EYFP fluorescent protein. Photobleaching experiments revealed a high mobility of YAP1 in the nucleus and the cytoplasm in both NFs and CAFs. These experiments also highlighted a constant and fast nucleocytoplasmic shuttling of the protein. Mathematical modelling analyses suggested a difference in the export rates from the nucleus to the cytoplasm, NFs showing a higher export rate than CAFs. This approach was extended to study the localisation, dynamics, and function of five YAP1 mutants. Analyses of the mutants showed differences in nuclear mobility and in export rates compared to the WT protein. Overall these data suggest the major roles of nuclear binding partners as well as export machinery in the regulation of YAP1 dynamics in NF1 and CAF1. In parallel, the role of YAP1 in fibroblasts during mouse development was assessed. Deletion of YAP1 in PDGFRα+ cells led to a lethal phenotype appearing at E11.5 due to haemorrhage in the head suggesting a crucial role of YAP1 protein in mesenchymal cells during normal vasculature development.
- Published
- 2016
4. Multisite assessment of reproducibility in high-content cell migration imaging data.
- Author
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Hu, J., Serra-Picamal, X., Bakker, G.J., Troys, M. Van, Winograd-Katz, S., Ege, N., Gong, X., Didan, Y., Grosheva, I., Polansky, O., Bakkali, K., Hamme, E. Van, Erp, M. van, Vullings, M., Weiss, Felix, Clucas, J., Dowbaj, A.M., Sahai, E., Ampe, C., Geiger, B., Friedl, P., Bottai, M., Strömblad, S., Hu, J., Serra-Picamal, X., Bakker, G.J., Troys, M. Van, Winograd-Katz, S., Ege, N., Gong, X., Didan, Y., Grosheva, I., Polansky, O., Bakkali, K., Hamme, E. Van, Erp, M. van, Vullings, M., Weiss, Felix, Clucas, J., Dowbaj, A.M., Sahai, E., Ampe, C., Geiger, B., Friedl, P., Bottai, M., and Strömblad, S.
- Abstract
Contains fulltext : 293806.pdf (Publisher’s version ) (Open Access), High-content image-based cell phenotyping provides fundamental insights into a broad variety of life science disciplines. Striving for accurate conclusions and meaningful impact demands high reproducibility standards, with particular relevance for high-quality open-access data sharing and meta-analysis. However, the sources and degree of biological and technical variability, and thus the reproducibility and usefulness of meta-analysis of results from live-cell microscopy, have not been systematically investigated. Here, using high-content data describing features of cell migration and morphology, we determine the sources of variability across different scales, including between laboratories, persons, experiments, technical repeats, cells, and time points. Significant technical variability occurred between laboratories and, to lesser extent, between persons, providing low value to direct meta-analysis on the data from different laboratories. However, batch effect removal markedly improved the possibility to combine image-based datasets of perturbation experiments. Thus, reproducible quantitative high-content cell image analysis of perturbation effects and meta-analysis depend on standardized procedures combined with batch correction.
- Published
- 2023
5. Expression of interleukin-8 and monocyte chemotactic protein 1 in women with endometriosis
- Author
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Ulukus, Murat, Ulukus, E. Cagnur, Tavmergen Goker, Ege N., Tavmergen, Erol, Zheng, Wenxin, and Arici, Aydin
- Published
- 2009
- Full Text
- View/download PDF
6. TENASCIN-C EXPRESSION IN ENDOMETRIOSIS
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Zekioglu, Osman, ULUKUŞ, EMİNE ÇAĞNUR, Goker, Ege N. Tavmergen, Tavmergen, Erol, Ulukus, Mustafa, Gundem, Gursen, and Ulukus, Murat
- Subjects
lcsh:R ,lcsh:Medicine ,lcsh:Gynecology and obstetrics ,lcsh:RG1-991 - Abstract
Objective: To investigate the expression of Tenascin-C (TN-C) in endometrium and endometriosis.
- Published
- 2005
7. İntrasitoplazmik sperm injeksiyonu uygulanan infertil olguda anormal sperm morfolojisi DNA hasarı ile birliktedir Olgu sunumu
- Author
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DURMAZ, AYŞEN, CİLAKER MIÇILI, SERAP, TAVMERGEN, EROL, DİKMEN, NURTEN, BAĞRIYANIK, HÜSNÜ ALPER, GÜNDÜZ, CUMHUR, VATANSEVER, HAFİZE SEDA, and TAVMERGEN GÖKER, EGE N
- Published
- 2011
8. Expression of the Bone Morphogenetic Protein-2 (BMP2) in the Human Cumulus Cells as a Biomarker of Oocytes and Embryo Quality.
- Author
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Demiray, Sirin B., Yilmaz, Ozlem, Goker, Ege N. T., Tavmergen, Erol, Calimlioglu, Nilufer, Sezerman, Ugur, Soykam, Huseyin O., and Oktem, Gulperi
- Subjects
BONE morphogenetic proteins ,TRANSFORMING growth factors-beta ,CUMULUS cells (Embryology) ,BIOMARKERS ,OVUM ,EMBRYOS - Abstract
Background: The members of the transforming growth factor-B superfamily, as the bone morphogenetic proteins (BMPs) subfamily and anti-Müllerian hormone (AMH), play a role during follicular development, and the bone morphogenetic protein-2 (BMP2), AMH, and THY1 are expressed in ovaries. Aim: This study was designed to define whether or not the expressions of these proteins in human cumulus cells (CCs) can be used as predictors of the oocyte and embryo competence. Settings and Design: The study included nine female patients who were diagnosed as idiopathic infertility, aged 25-33 years (median 30 years) and underwent Assisted Reproductive Technologies. Materials and Methods: The CCs from 60 oocyte-cumulus complexes obtained from the nine patients were evaluated with immunofluorescence staining in respect of BMPs, AMH and THY1 markers. The CCs surrounding the same oocytes were evaluated separately according to the oocyte and embryo quality. Statistical Analysis: Quantitative data were statistically analyzed for differences using the two-sided Mann-Whitney U test (P < 0.05). Results and Conclusions: Significant differences in immunofluorescence staining were observed in oocyte quality and embryo quality for the BMP2 only (P < 0.05). No significant differences were observed for AMH or CD90/THY1. Conclusion: These results demonstrated that there is a significant difference in the expression of BMP2 in the CCs of good quality oocytes and subsequently a good embryo. [ABSTRACT FROM AUTHOR]
- Published
- 2017
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9. Early and midluteal phase blood estradiol levels after ovum pickup and pregnancy rates after ICSI cycles
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Rafael, Levi, S Eser, Ozyurek, Ege N Tavmergen, Goker, and Erol H, Tavmergen
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Male ,Chi-Square Distribution ,Estradiol ,Pregnancy Rate ,Enzyme-Linked Immunosorbent Assay ,Luteal Phase ,Embryo Transfer ,Chorionic Gonadotropin ,Statistics, Nonparametric ,Predictive Value of Tests ,Pregnancy ,Humans ,Female ,Prospective Studies ,Sperm Injections, Intracytoplasmic ,Biomarkers ,Progesterone - Abstract
To examine whether blood estradiol level tendencies during the late follicular and early luteal phases and the 11 days after embryo transfer have any association with the outcome of intracytoplasmic sperm injection-embryo transfer (ICSI-ET) cycles.This prospective study involved 38 assisted reproductive technology cycles in 35 infertile patients treated with assisted reproductive technologies in which blood samples taken on the 4th, 7th, 9th and 11th days following ET were tested for progesterone, estradiol and hCG levels using an enzyme-linked immunoassay. The estradiol blood levels were compared with the maximal follicular phase blood estradiol. The data were analyzed using Microsoft Excel (Redmond, Washington) and SPSS 10.0 (Chicago, Illinois). The chi2, Mann-Whitney U, Wilcoxon and Pearson tests were usedfor statistical analysis.Average maximum estradiol blood level, number of oocytes produced,fertilization rates and cleavage rates did not show any significant difference between pregnant and nonpregnant cycles. The lower the ratios of estradiol levels measured on posttransfer days 4, 7 and 9 to the maximumfollicular phase level, the lower the probability of pregnancy (P.01, P.01 and P.01, respectively).The steeper the decline in blood estradiol levels (affecting the periimplantation period) following ovum pickup relative to the maximum follicular phase estradiol levels, the lower the chance of pregnancy in ICSI-ET cycles.
- Published
- 2004
10. İn-vitro fertilizasyon embriyo transferi sikluslarında HCG uygulaması sonrası estradiol cevabı siklus başarısını öngörebilir mi?
- Author
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Levı, Rafael, Özçakır, H. Tayfun, Çebi, Ziya, Küpelioğlu, Latif, Adakan, Şaban, Tavmergen, Erol, Göker, Ege N. T., and Ege Üniversitesi
- Subjects
Cerrahi - Abstract
Amaç: İn-vitro fertilizasyon embryo transferi(IVF-ET) sikluslannda human chorionic gondotropin (HCG) uygulandıktan sonra estradiol (E2) oranlarında gözlenen değişim derecesine göre fertilizasyon oranlarının ve gebelik oranlarının etkilenip etkilenmediğini araştırmak. Çalışmanın Yapıldığı Yer: Ege Üniversitesi, Aile Planlaması, İnfertilite Araştırma ve Uygulama Merkezi, Bornova, İzmir Materyal ve Method: IVF-ET uygulanan 248 olgu çalışma kapsamına alındı. Hastalar HCG uygulama öncesi ve sonrasında ölçülen estradiol seviyelerinin oranlanmasına göre sınıflandırılarak E2 düzeyi %10'dan fazla artanlar grup-1, E2 seviyesi öncekine göre %10'dan daha az artan yada azalanlar grup-2 ve E2 düzeyi öncekine göre %10'dan fazla düşenler grup-3 olmak üzere 3 gruba ayrıldı. Gruplarda, alınan oositlerin kaliteleri, fertilizasyon oranlan ve klinik gebelik oranları karşılaştırıldı. Bulgular: Gruplar arasında elde edilen ortalama metafaz-II oosit sayılarında anlamlı fark yoktu (sırasıyla; 7.4, 8.3, 8.5), (p=0.248). Fertilizasyon oranları her üç grupta da benzerdi; (sırasıyla; %76, %78, %80). Klinik gebelik o-ranları gruplarda sırasıyla %35.0 (50/143), %32.9 (26/79) ve %30.8 (8/26) bulundu ve istatistiksel olarak anlamlı değildi. Sonuç: Çalışma grubumuzda elde edilen sonuçlara göre IVF-ET sikluslannda HCG uygulaması sonrası E2 seviyesinde meydana gelen değişiklikler ile oosit kalitesi, fertilizasyon oranları ve klinik gebelik oranları arasında korelasyon saptanamadı., Objective: To analyse the effect of the changes in serum estradiol (E2) concentrations after human chorionic gonadotopin administration(HCG) on fertilization rate and pregnancy rate in in-vitro fertilization embryo transfer(IVF-ET) cycles. Setting: Ege University, Family Planning, Infertility Research and Treatment Center, Bornova, İzmir, Turkey Matherial and Method: Two-hundred-forty-eight patients who had undergone IVF-ET were enrolled into the study. the patients were grouped according to the ratio of serum E2 levels before and after HCG administration; group-1 consisted of the patients who had an increase in E2 of >10%, group-2 with E2 levels remained between a gain and loss of 10%, and group-3 responders exhibited a >10% decrease in their E2 levels after HCG. the primary outcome measures included the oocyte quality, the fertilization rates and the clinical pregnancy rates. Results: There was no difference in terms of the mean number of metaphase-II oocytes picked up among the groups (7.4, 8.3, 8.5, repectively),(p=0.248). the fertilization rates in group-1, group-2, and group-3 were found to be similar(76%, 78%, 80%, respectively),(p=0,833). the clinical pregnancy rates in group-1, group-2, and group-3 were 35.0% (50/143), 32.9.0% (26/79), and 30.8% (8/26), respectively and there was no statistically significant difference (p=0.896). Conclusion: in our study population, the results do not ascribe any predictive significance of E2 response after HCG administration to oocyte quality, fertilization rates and clinical pregnancy rates in IVF-ET cycles.
- Published
- 2003
11. What is the role of endoscopy in the evaluationof adnexal masses
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Tavmergen, Erol, Adakan, Şaban, Levı, Rafael, Göker, Tavmergen Ege N., and Ege Üniversitesi
- Subjects
0-Belirlenecek - Abstract
Amaç: Adneksiyal kitlelerin tanısında ve tedavisinde endoskopinin yerini değerlendirmek Çalışmanın Yapıldığı Yer: Ege Üniversitesi Rektörlüğü Aile Planlaması İnfertilite Araştırma ve Uygulama Merkezi, İzmir Materyal ve Metod: Merkezimize infertilite nedeni ile başvuran hastalardan jinekolojik muayene ve ultrasonografik tarama ile adneksiyal kitle saptanmış olgular değerlendirildi. Doppler USG ve tümör belirteçleri malignite kriteri içermeyen 112 olgu endoskopik olarak incelendi. Tüm endoskopik işlemler genel anestezi altında ve steril şartlarda yapıldı. Göbek hizasından 10 mm trokar içinden 0? optik ile pelvis görüntülendi. Suprasynfizer hizadan 5 veya 10 mm’lik trokarlar ile operasyon tamamlandı. Bulgular: Ovaryan kitlelerin tanısı ve rastlanma sıklıkları ile yapılan operasyonlar tabloda verilmiştir (endometrioma %64,5 ; dermoid kist %7,2 ; seröz kistadenom %1,8 ; musinöz kistadenom %0,9 ; fonksiyonel over kisti %17,3 ; paraovarian kist %8,1). Olgulardan 2 (%1,7)’sinde laparatomiye dönülmüştür. Diğer olgularda cerrahi işlemler laparoskopik olarak sonuçlandırılmıştır. Sonuçlar:Laparoskopi, laparatomiye göre hospitalizasyon ve ambulasyon süresinin daha kısa olması, pelvik organlarda ve abdomende daha az adezyon formasyonuna neden olması ile daha avantajlı bir müdahaledir., Objective: the purpose of this study was to evaluate the role of endoscopy in the diagnosis and treatment of adnexal masses. Materials and Methods: the patients who admitted to our clinic for infertility and having adnexal masses diagnosed by pelvic examination and ultrasonography were included to this study. A hundred and twelve patients whose tumoral markers were normal, and without malignant criteria in doppler ultrasonography were assessed by endoscopy. Pelvis were examined by 0∞ optic by 10 mm umbilical trocar. Surgical operations were performed by using suprasymphysial 5 mm or 10 mm trocars. Results: the pathologic diagnosis of ovarian masses were as follows: endometrioma, 64,5%; dermoid cyst, 7.2%; serous cystadenoma, 1.8%; mucinous cystadenoma, 0.9%; functional ovarian cyst, 17.3%; and paraovarian cyst, 8.1%. in two (1.7%) patients laparotomy was needed for exact excision of the adnexal masses. All the remaining patients were completely treated by laparoscopy. Conclusion:Laparoscopy is more advantageous than laparotomy with respect to hospitalisation and ambulation times, and adhesion formation in pelvic and abdominal viscera.
- Published
- 2003
12. Comparison of the ICSI outcome of ejaculated sperm with normal, abnormal parameters and testicular sperm
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Göker, Ege N. Tavmergen, Sendag, Fatih, Levi, Rafael, Sendag, Handan, Tavmergen, Erol, and Göker, Ege N Tavmergen
- Subjects
- *
PREGNANCY , *SEMEN - Abstract
Objective(s): To compare fertilization rates, quality of embryos, pregnancy rates (PRs) and outcome of pregnancies in intracytoplasmic sperm injection (ICSI) using sperm from ejaculates of normal and abnormal semen and testicular sperm of non-obstructive azoospermia. Study design: Four hundred fifty-four patients who underwent 454 ICSI cycles were evaluated retrospectively. Patients were divided into three groups according to the quality and source of sperm. Patients in group 1 underwent 133 cycles of ICSI using ejaculated normal semen, group 2 underwent 235 cycles using ejaculated abnormal semen, and group 3 underwent 86 cycles using testicular sperm. Results: The parameters were compared among the groups with respect to cycles induced by long (
n=160 ) and short (n=294 ) protocol. In group 3, the fertilization and PRs were significantly lower than in all other groups (51.3 and 10.6% in the long protocol cycles, 53.3 and 5.1% in the short protocol cycles, respectively). There was no significant difference in the outcome of pregnancies in respect to abortion rates between different groups. Conclusion(s): The fertilizing ability of sperm in ICSI is highest with ejaculated sperm and lowest with sperm extracted by testicular biopsy. Also, the clinical PRs are significantly lower in ICSI with sperm from testicular biopsy. However, the outcomes of pregnancies are not affected by using surgically retrieved sperm from ejaculated semen. [Copyright &y& Elsevier]- Published
- 2002
- Full Text
- View/download PDF
13. 200 Breast Cancer-associated Fibroblasts Activated State is Regulated by Yes-associated Protein Activation Induced by Matrix Stiffness and Cytoskeletal Contractility
- Author
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Calvo, F., primary, Ege, N., additional, Jenkins, R., additional, Hooper, S., additional, Grande-Garcia, A., additional, Moeendarbary, E., additional, Charras, G., additional, and Sahai, E., additional
- Published
- 2012
- Full Text
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14. Gluteal Artery Pseudoaneurysm, a Rare Cause of Sciatic Pain
- Author
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Yurtseven, Taşkin, primary, Zileli, Mehmet, additional, Tavmergen Göker, Ege N., additional, Tavmergen, Erol, additional, Hoşcoşkun, Cüneyt, additional, and Parildar, Mustafa, additional
- Published
- 2002
- Full Text
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15. Unilateral Ectopic Twin Pregnancy Following an IVF Cycle
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Göker, Ege N. Tavmergen, primary, Tavmergen, Erol, additional, Özçakir, H. Tayfun, additional, Levi, Rafael, additional, and Adakan, Şaban, additional
- Published
- 2001
- Full Text
- View/download PDF
16. Ligneous Cervicovaginitis Associated with Plasminogen Deficiency: A Rare Cause of Infertility.
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AKDOGAN, Aysin, SAHIN, Gulnaz, AKMAN, Levent, SIMSEK, Deniz, ZEKIOGLU, Osman, GOKER, Ege N. T., and TAVMERGEN, Erol
- Subjects
- *
INFERTILITY , *DYSMENORRHEA , *VAGINAL discharge , *PATIENTS - Abstract
A letter to the editor is presented which discusses ligneous inflammation diagnosis in a 27-year-old female patient suffering infertility, dysmenorrhea, and heavy vaginal discharge.
- Published
- 2015
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17. Ammonothermal Crystal Growth of Functional Nitrides for Semiconductor Devices: Status and Potential.
- Author
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Wostatek T, Chirala VYMR, Stoddard N, Civas EN, Pimputkar S, and Schimmel S
- Abstract
The state-of-the-art ammonothermal method for the growth of nitrides is reviewed here, with an emphasis on binary and ternary nitrides beyond GaN. A wide range of relevant aspects are covered, from fundamental autoclave technology, to reactivity and solubility of elements, to synthesized crystalline nitride materials and their properties. Initially, the potential of emerging and novel nitrides is discussed, motivating their synthesis in single crystal form. This is followed by a summary of our current understanding of the reactivity/solubility of species and the state-of-the-art single crystal synthesis for GaN, AlN, AlGaN, BN, InN, and, more generally, ternary and higher order nitrides. Investigation of the synthesized materials is presented, with a focus on point defects (impurities, native defects including hydrogenated vacancies) based on GaN and potential pathways for their mitigation or circumvention for achieving a wide range of controllable functional and structural material properties. Lastly, recent developments in autoclave technology are reviewed, based on GaN, with a focus on advances in development of in situ technologies, including in situ temperature measurements, optical absorption via UV/Vis spectroscopy, imaging of the solution and crystals via optical (visible, X-ray), along with use of X-ray computed tomography and diffraction. While time intensive to develop, these technologies are now capable of offering unprecedented insight into the autoclave and, hence, facilitating the rapid exploration of novel nitride synthesis using the ammonothermal method.
- Published
- 2024
- Full Text
- View/download PDF
18. Emergent mechanical control of vascular morphogenesis.
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Whisler J, Shahreza S, Schlegelmilch K, Ege N, Javanmardi Y, Malandrino A, Agrawal A, Fantin A, Serwinski B, Azizgolshani H, Park C, Shone V, Demuren OO, Del Rosario A, Butty VL, Holroyd N, Domart MC, Hooper S, Szita N, Boyer LA, Walker-Samuel S, Djordjevic B, Sheridan GK, Collinson L, Calvo F, Ruhrberg C, Sahai E, Kamm R, and Moeendarbary E
- Subjects
- Mice, Animals, Tissue Engineering methods, Morphogenesis, Cell Differentiation, Extracellular Matrix, Mechanotransduction, Cellular physiology, Endothelial Cells
- Abstract
Vascularization is driven by morphogen signals and mechanical cues that coordinately regulate cellular force generation, migration, and shape change to sculpt the developing vascular network. However, it remains unclear whether developing vasculature actively regulates its own mechanical properties to achieve effective vascularization. We engineered tissue constructs containing endothelial cells and fibroblasts to investigate the mechanics of vascularization. Tissue stiffness increases during vascular morphogenesis resulting from emergent interactions between endothelial cells, fibroblasts, and ECM and correlates with enhanced vascular function. Contractile cellular forces are key to emergent tissue stiffening and synergize with ECM mechanical properties to modulate the mechanics of vascularization. Emergent tissue stiffening and vascular function rely on mechanotransduction signaling within fibroblasts, mediated by YAP1. Mouse embryos lacking YAP1 in fibroblasts exhibit both reduced tissue stiffness and develop lethal vascular defects. Translating our findings through biology-inspired vascular tissue engineering approaches will have substantial implications in regenerative medicine.
- Published
- 2023
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19. Multisite assessment of reproducibility in high-content cell migration imaging data.
- Author
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Hu J, Serra-Picamal X, Bakker GJ, Van Troys M, Winograd-Katz S, Ege N, Gong X, Didan Y, Grosheva I, Polansky O, Bakkali K, Van Hamme E, van Erp M, Vullings M, Weiss F, Clucas J, Dowbaj AM, Sahai E, Ampe C, Geiger B, Friedl P, Bottai M, and Strömblad S
- Subjects
- Cell Movement, Reproducibility of Results
- Abstract
High-content image-based cell phenotyping provides fundamental insights into a broad variety of life science disciplines. Striving for accurate conclusions and meaningful impact demands high reproducibility standards, with particular relevance for high-quality open-access data sharing and meta-analysis. However, the sources and degree of biological and technical variability, and thus the reproducibility and usefulness of meta-analysis of results from live-cell microscopy, have not been systematically investigated. Here, using high-content data describing features of cell migration and morphology, we determine the sources of variability across different scales, including between laboratories, persons, experiments, technical repeats, cells, and time points. Significant technical variability occurred between laboratories and, to lesser extent, between persons, providing low value to direct meta-analysis on the data from different laboratories. However, batch effect removal markedly improved the possibility to combine image-based datasets of perturbation experiments. Thus, reproducible quantitative high-content cell image analysis of perturbation effects and meta-analysis depend on standardized procedures combined with batch correction., (© 2023 The Authors. Published under the terms of the CC BY 4.0 license.)
- Published
- 2023
- Full Text
- View/download PDF
20. Green's functions for a layered high-contrast acoustic media.
- Author
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Özdemir Ö, Yücel H, Uçar YE, Erbaş B, and Ege N
- Abstract
A parametric approach based on parametric analysis of the acoustical properties of a layered media is proposed to derive a reduced layered Green's function. The approach relies on the smallness of one of the problem parameters and allows a simpler form of Green's function by disregarding the smaller parametric terms. Several illustrative examples comparing the amplitudes of exact and reduced Green's function for small parameter of density ratio in various source and observation location setups are presented. It is demonstrated that the CPU times calculated at different points decrease considerably for the reduced Green's function, further justifying the presented method.
- Published
- 2022
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21. Phenotypic screening with target identification and validation in the discovery and development of E3 ligase modulators.
- Author
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Ege N, Bouguenina H, Tatari M, and Chopra R
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- Drug Evaluation, Preclinical, Humans, Immunologic Factors chemistry, Phenotype, Drug Development, Immunologic Factors pharmacology, Ubiquitin-Protein Ligases metabolism
- Abstract
The use of phenotypic screening was central to the discovery and development of novel thalidomide analogs, the IMiDs (immunomodulatory drugs) agents. With the discovery that these agents bind the E3 ligase, CRL4
CRBN , and alter its substrate specificity, there has been a great deal of endeavor to discover other small molecules that can modulate alternative E3 ligases. Furthermore, the chemical properties necessary for drug discovery and the rules by which neo-substrates are selected for degradation are being defined in the context of phenotypic alterations in specific cellular systems. This review gives a detailed summary of these recent advances and the methodologies being exploited to understand the mechanism of action of emerging protein degradation therapies., Competing Interests: Declaration of interests The authors declare no competing interests. R.C. is a former employee of Celgene Corporation and previously had commercial interest in IMiDs, and is also a founder of Monte Rosa Therapeutics., (Copyright © 2021 Elsevier Ltd. All rights reserved.)- Published
- 2021
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22. Quantitative Analysis Reveals that Actin and Src-Family Kinases Regulate Nuclear YAP1 and Its Export.
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Ege N, Dowbaj AM, Jiang M, Howell M, Hooper S, Foster C, Jenkins RP, and Sahai E
- Subjects
- Actins genetics, Active Transport, Cell Nucleus physiology, Adaptor Proteins, Signal Transducing genetics, Adaptor Proteins, Signal Transducing physiology, Animals, Cell Cycle Proteins, Cell Line, Tumor, Cell Movement, Cell Nucleus metabolism, Cell Proliferation, Cytoplasm metabolism, Cytoskeleton metabolism, DNA-Binding Proteins genetics, Fibroblasts metabolism, Gene Expression Regulation, Humans, Mice, Models, Theoretical, Phosphoproteins genetics, Phosphoproteins physiology, Phosphorylation, Photobleaching, Signal Transduction, YAP-Signaling Proteins, src-Family Kinases genetics, Actins metabolism, Adaptor Proteins, Signal Transducing metabolism, Phosphoproteins metabolism, src-Family Kinases metabolism
- Abstract
The transcriptional regulator YAP1 is critical for the pathological activation of fibroblasts. In normal fibroblasts, YAP1 is located in the cytoplasm, while in activated cancer-associated fibroblasts, it is nuclear and promotes the expression of genes required for pro-tumorigenic functions. Here, we investigate the dynamics of YAP1 shuttling in normal and activated fibroblasts, using EYFP-YAP1, quantitative photobleaching methods, and mathematical modeling. Imaging of migrating fibroblasts reveals the tight temporal coupling of cell shape change and altered YAP1 localization. Both 14-3-3 and TEAD binding modulate YAP1 shuttling, but neither affects nuclear import. Instead, we find that YAP1 nuclear accumulation in activated fibroblasts results from Src and actomyosin-dependent suppression of phosphorylated YAP1 export. Finally, we show that nuclear-constrained YAP1, upon XPO1 depletion, remains sensitive to blockade of actomyosin function. Together, these data place nuclear export at the center of YAP1 regulation and indicate that the cytoskeleton can regulate YAP1 within the nucleus., (Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.)
- Published
- 2018
- Full Text
- View/download PDF
23. Mechanotransduction and YAP-dependent matrix remodelling is required for the generation and maintenance of cancer-associated fibroblasts.
- Author
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Calvo F, Ege N, Grande-Garcia A, Hooper S, Jenkins RP, Chaudhry SI, Harrington K, Williamson P, Moeendarbary E, Charras G, and Sahai E
- Subjects
- Actin Cytoskeleton, Actomyosin metabolism, Adaptor Proteins, Signal Transducing genetics, Animals, Cell Cycle Proteins, Cells, Cultured, Disease Progression, Enzyme Activation, Extracellular Matrix metabolism, Female, Focal Adhesions, Humans, Mice, Microscopy, Atomic Force, Microtubule-Associated Proteins metabolism, Myosin Light Chains, NADPH Dehydrogenase metabolism, Neoplasm Invasiveness, Neovascularization, Pathologic, Phosphoproteins genetics, Phosphorylation, RNA Interference, RNA, Small Interfering, YAP-Signaling Proteins, rho-Associated Kinases antagonists & inhibitors, src-Family Kinases metabolism, Adaptor Proteins, Signal Transducing metabolism, Breast Neoplasms metabolism, Fibroblasts physiology, Mechanotransduction, Cellular, Phosphoproteins metabolism
- Abstract
To learn more about cancer-associated fibroblasts (CAFs), we have isolated fibroblasts from different stages of breast cancer progression and analysed their function and gene expression. These analyses reveal that activation of the YAP transcription factor is a signature feature of CAFs. YAP function is required for CAFs to promote matrix stiffening, cancer cell invasion and angiogenesis. Remodelling of the ECM and promotion of cancer cell invasion requires the actomyosin cytoskeleton. YAP regulates the expression of several cytoskeletal regulators, including ANLN and DIAPH3, and controls the protein levels of MYL9 (also known as MLC2). Matrix stiffening further enhances YAP activation, thus establishing a feed-forward self-reinforcing loop that helps to maintain the CAF phenotype. Actomyosin contractility and Src function are required for YAP activation by stiff matrices. Further, transient ROCK inhibition is able to disrupt the feed-forward loop, leading to a long-lasting reversion of the CAF phenotype.
- Published
- 2013
- Full Text
- View/download PDF
24. Loss of T cell CD98 H chain specifically ablates T cell clonal expansion and protects from autoimmunity.
- Author
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Cantor J, Slepak M, Ege N, Chang JT, and Ginsberg MH
- Subjects
- Adoptive Transfer, Animals, Autoimmune Diseases pathology, Clone Cells, Diabetes Mellitus, Experimental genetics, Diabetes Mellitus, Experimental immunology, Diabetes Mellitus, Experimental prevention & control, Diabetes Mellitus, Type 1 genetics, Diabetes Mellitus, Type 1 immunology, Diabetes Mellitus, Type 1 prevention & control, Humans, Integrin beta Chains chemistry, Integrin beta Chains physiology, Mice, Mice, Knockout, Mice, Transgenic, Protein Structure, Tertiary genetics, T-Lymphocyte Subsets transplantation, Autoimmune Diseases genetics, Autoimmune Diseases prevention & control, Cell Proliferation, Fusion Regulatory Protein 1, Heavy Chain genetics, T-Lymphocyte Subsets immunology, T-Lymphocyte Subsets pathology
- Abstract
CD98 H chain (4F2 Ag, Slc3a2) was discovered as a lymphocyte-activation Ag. Deletion of CD98 H chain in B cells leads to complete failure of B cell proliferation, plasma cell formation, and Ab secretion. In this study, we examined the role of T cell CD98 in cell-mediated immunity and autoimmune disease pathogenesis by specifically deleting it in murine T cells. Deletion of T cell CD98 prevented experimental autoimmune diabetes associated with dramatically reduced T cell clonal expansion. Nevertheless, initial T cell homing to pancreatic islets was unimpaired. In sharp contrast to B cells, CD98-null T cells showed only modestly impaired Ag-driven proliferation and nearly normal homeostatic proliferation. Furthermore, these cells were activated by Ag, leading to cytokine production (CD4) and efficient cytolytic killing of targets (CD8). The integrin-binding domain of CD98 was necessary and sufficient for full clonal expansion, pointing to a role for adhesive signaling in T cell proliferation and autoimmune disease. When we expanded CD98-null T cells in vitro, they adoptively transferred diabetes, establishing that impaired clonal expansion was responsible for protection from disease. Thus, the integrin-binding domain of CD98 is required for Ag-driven T cell clonal expansion in the pathogenesis of an autoimmune disease and may represent a useful therapeutic target.
- Published
- 2011
- Full Text
- View/download PDF
25. Early and midluteal phase blood estradiol levels after ovum pickup and pregnancy rates after ICSI cycles.
- Author
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Levi R, Ozyurek SE, Goker EN, and Tavmergen EH
- Subjects
- Biomarkers blood, Chi-Square Distribution, Enzyme-Linked Immunosorbent Assay, Female, Humans, Male, Predictive Value of Tests, Pregnancy, Prospective Studies, Sperm Injections, Intracytoplasmic, Statistics, Nonparametric, Chorionic Gonadotropin blood, Embryo Transfer, Estradiol blood, Luteal Phase blood, Pregnancy Rate, Progesterone blood
- Abstract
Objective: To examine whether blood estradiol level tendencies during the late follicular and early luteal phases and the 11 days after embryo transfer have any association with the outcome of intracytoplasmic sperm injection-embryo transfer (ICSI-ET) cycles., Study Design: This prospective study involved 38 assisted reproductive technology cycles in 35 infertile patients treated with assisted reproductive technologies in which blood samples taken on the 4th, 7th, 9th and 11th days following ET were tested for progesterone, estradiol and hCG levels using an enzyme-linked immunoassay. The estradiol blood levels were compared with the maximal follicular phase blood estradiol. The data were analyzed using Microsoft Excel (Redmond, Washington) and SPSS 10.0 (Chicago, Illinois). The chi2, Mann-Whitney U, Wilcoxon and Pearson tests were usedfor statistical analysis., Results: Average maximum estradiol blood level, number of oocytes produced,fertilization rates and cleavage rates did not show any significant difference between pregnant and nonpregnant cycles. The lower the ratios of estradiol levels measured on posttransfer days 4, 7 and 9 to the maximumfollicular phase level, the lower the probability of pregnancy (P < .01, P < .01 and P < .01, respectively)., Conclusion: The steeper the decline in blood estradiol levels (affecting the periimplantation period) following ovum pickup relative to the maximum follicular phase estradiol levels, the lower the chance of pregnancy in ICSI-ET cycles.
- Published
- 2004
26. A modified metabolic inhibition test for the titration of poliovirus neutralizing antibodies.
- Author
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MUSSETT MV, DIMIC M, EGE N, and TOBIN JO
- Subjects
- Humans, Antibodies, Neutralizing, Enterovirus C, Human, Poliomyelitis diagnosis, Poliovirus
- Published
- 1961
- Full Text
- View/download PDF
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