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Article ; Online: Distinct patterns of sedimentary phosphorus fractionation and mobilization in the seafloor of the Black Sea, Marmara Sea and Mediterranean Sea

Akçay, İsmail / Yücel, Mustafa

Science of the Total Environment. 2023 Mar., v. 863 p.160936-

2023

Abstract: Phosphorus (P) is a key element to all life that is used for structural and functional component of all organisms. The cycling of sedimentary P may differ depending on the redox-conditions of the overlying waters affecting the dynamics, and distribution ... ...

Abstract	Phosphorus (P) is a key element to all life that is used for structural and functional component of all organisms. The cycling of sedimentary P may differ depending on the redox-conditions of the overlying waters affecting the dynamics, and distribution of P-fractions and the elements that are highly coupled to P cycle. Though biogeochemistry of water column in the three interconnected marine basins of Black, Marmara and Mediterranean Seas have been studied extensively, few studies were carried out to understand sedimentary P dynamics in these regions. In this study, therefore, the biogeochemical cycling of sedimentary P and related variables such as porewater nutrients, sedimentary organic carbon, nitrogen and reactive iron were studied in selected sites at the three interconnected marine basins: Black Sea, Marmara and Northeastern (NE) Mediterranean Sea. The pool of “potentially mobile P” was also determined for the studied sites. The study results showed that porewater and sediment biogeochemistry displayed great variability in the studied sites with the maximum concentrations of porewater phosphate, ammonium, reactive silicate, surface sediment organic carbon, nitrogen, phosphorus and total phosphorus (TP) measured in the hypoxic Marmara Sea and suboxic/anoxic Black Sea. The decline in the TP concentrations of all sediment core samples indicated P-mobilization to the overlying water. The pool of “potentially mobile P” varied between 0.023 and 0.148 mol/m² in the studied sites with the maximum values recorded in suboxic and anoxic/sulfidic parts of the Black Sea. This study predicts that the deoxygenation and eutrophication would further lead to the preferential release of P in these three interconnected marine basins, hence changing the remineralization, N/P molar ratios and eventually transform the deep-water nutrient stocks with implications for internal N/P control on marine ecosystems.
Keywords	ammonium ; biogeochemistry ; environment ; eutrophication ; fractionation ; iron ; nitrogen ; organic carbon ; phosphates ; phosphorus ; sediments ; silicates ; total phosphorus ; Black Sea ; Marmara Sea ; Mediterranean Sea ; Sedimentary phosphorus cycle ; Potentially mobile phosphorus ; Northeastern Mediterranean Sea
Language	English
Dates of publication	2023-03
Publishing place	Elsevier B.V.
Document type	Article ; Online
ZDB-ID	121506-1
ISSN	1879-1026 ; 0048-9697
ISSN (online)	1879-1026
ISSN	0048-9697
DOI	10.1016/j.scitotenv.2022.160936
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Pulmonary Embolism in a Liver Donor: A Case Report and Review of the Literature.

Esendagli, Dorina / Akcay, Sule / Yildirim, Sedat / Haberal, Mehmet

Experimental and clinical transplantation : official journal of the Middle East Society for Organ Transplantation

2023 Volume 21, Issue 10, Page(s) 851–853

Abstract: Liver transplant is an important treatment option for end-stage liver disease, and living related donation is an option to shorten or eliminate the waiting period for the patients, especially when shortage of organs is of concern. It is crucial to ... ...

Abstract	Liver transplant is an important treatment option for end-stage liver disease, and living related donation is an option to shorten or eliminate the waiting period for the patients, especially when shortage of organs is of concern. It is crucial to provide optimal safety for the donors and to thoroughly examine them preoperatively in order to decrease perioperative and postoperative complications. Here, we report the case of a living donor who had undergone a left liver lobectomy and on postoperative day 2 presented with a radiologically severe pulmonary embolism, despite the absence of any risk factor for venous thromboembolism or pulmonary embolism. The patient was treated with tissue plasminogen activator and heparin infusions and was discharged 1 week later.
MeSH term(s)	Humans ; Tissue Plasminogen Activator ; Living Donors ; Pulmonary Embolism/diagnostic imaging ; Pulmonary Embolism/etiology ; Pulmonary Embolism/surgery ; Hepatectomy/adverse effects ; Liver
Chemical Substances	Tissue Plasminogen Activator (EC 3.4.21.68)
Language	English
Publishing date	2023-07-27
Publishing country	Turkey
Document type	Review ; Case Reports ; Journal Article
ZDB-ID	2396778-X
ISSN	2146-8427 ; 1304-0855
ISSN (online)	2146-8427
ISSN	1304-0855
DOI	10.6002/ect.2023.0098
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Article ; Online: Non-negative matrix factorization and differential expression analyses identify hub genes linked to progression and prognosis of glioblastoma multiforme.

Akçay, Sevinç / Güven, Emine / Afzal, Muhammad / Kazmi, Imran

Gene

2022 Volume 824, Page(s) 146395

Abstract: One of the most prevailing primary brain tumors in adult human male is glioblastoma multiforme (GBM), which is categorized by rapid cellular growth. Even though the combination therapy comprises surgery, chemotherapy, and adjuvant therapies, the survival ...

Abstract	One of the most prevailing primary brain tumors in adult human male is glioblastoma multiforme (GBM), which is categorized by rapid cellular growth. Even though the combination therapy comprises surgery, chemotherapy, and adjuvant therapies, the survival rate, on average, is 14.6 months. Glioma stem cells (GSCs) have key roles in tumorigenesis, progression, and defiance against chemotherapy and radiotherapy. In our study, firstly, the gene expression dataset GSE124145 was retrieved; the non-negative matrix factorization (NMF) method was applied on GBM dataset, and differentially expressed genes analysis (DEGs) was performed. After which, overlapping genes between metagenes and DEGs were detected to examine the Gene Ontology (GO) categories in the biological process (BP) in the stemness of GBM. The common hub genes were used to construct protein-protein interaction (PPI) network and further GO, while Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway was utilized to pinpoint the real hub genes. The analysis of hub genes particular for the same GO categories demonstrated that specific hub genes triggered distinct features of the same biological processes. After utilizing GSE124145 and The Cancer Genome Atlas (TCGA) dataset for survival analysis, we screened five real hub genes: GUCA1A, RFC2, GNG11, MMP19, and NRG1, which are strongly associated with the progression and prognosis of GBM. The DEGs analysis revealed that all real hub genes were overexpressed in GBM and TCGA datasets, which further validates our results. The constructed study of PPI, GO, and KEGG pathway on common hub genes was performed. Finally, the KEGG pathways performed on the top 15 candidate hub genes (including six real hub genes) of the PPI network in the GBM gene expression dataset study found mitogen-activated protein kinase (Mapk) signaling pathway to be the most significant pathway. The rest of the hub genes reviewed throughout the analysis might be favorable targets for diagnosing and treating GBM and lower-grade gliomas.
MeSH term(s)	Adult ; Brain Neoplasms/pathology ; Computational Biology/methods ; Gene Expression Regulation, Neoplastic ; Gene Regulatory Networks ; Glioblastoma/metabolism ; Glioma/genetics ; Humans ; Male ; Protein Interaction Maps/genetics
Language	English
Publishing date	2022-03-11
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	391792-7
ISSN	1879-0038 ; 0378-1119
ISSN (online)	1879-0038
ISSN	0378-1119
DOI	10.1016/j.gene.2022.146395
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Article ; Online: Is Kinesio Taping Effective for Knee Osteoarthritis? Randomised, Controlled, Double-blind Study.

Dogan, Nesibe / Yilmaz, Hayriye / Ince, Bugra / Akcay, Seniz

Journal of the College of Physicians and Surgeons--Pakistan : JCPSP

2022 Volume 32, Issue 11, Page(s) 1441–1447

Abstract: Objective: To determine the effects of Kinesio taping on pain, functional performance, range of motion, and postural stability in patients with knee osteoarthritis.: Study design: Randomised double-blind controlled trial.: Place and duration of ... ...

Abstract	Objective: To determine the effects of Kinesio taping on pain, functional performance, range of motion, and postural stability in patients with knee osteoarthritis. Study design: Randomised double-blind controlled trial. Place and duration of study: Department of Physical Medicine and Rehabilitation, University of Health Sciences, Izmir Bozyaka Training and Research Hospital, Turkey, from November 2019 to October 2021. Methodology: Fifty-seven patients with knee osteoarthritis (grade II or higher) according to the Kellgren-Lawrence classification received Kinesio tape or sham-Kinesio tape on the rectus femoris muscle three times a week. Patients were evaluated using the visual analogue scale (VAS), Western ontario and McMaster Universities Osteoarthritis Index (WOMAC), 50-meter walk time, range of motion (ROM), and postural stability index at baseline, 1st hour, 3rd week, 7th week. A mixed model analysis of repeated measures was used to test the effect of KT on outcome measures. Calculations were based on an intention-to-treat analysis. Results: The only significant difference between groups was in the dynamic medio-lateral stability index [F (2.6,144.1)=3.83, p=0.015], indicating the inferiority of KT at week 3. There were differences within groups in 50-meter walking time and VAS at rest, which showed improvements over time in both groups. No significant difference was found between or within groups for other outcomes. Conclusion: The KT intervention for three consecutive weeks showed no superiority over sham-KT in terms of pain intensity, knee-related health status, knee ROM, functional performance, and postural stability. Key words: Kinesio taping, Knee osteoarthritis, Pain, Gait, Functions.
MeSH term(s)	Humans ; Athletic Tape ; Double-Blind Method ; Muscle Strength/physiology ; Osteoarthritis, Knee/therapy ; Pain/etiology ; Range of Motion, Articular/physiology ; Treatment Outcome
Language	English
Publishing date	2022-11-14
Publishing country	Pakistan
Document type	Randomized Controlled Trial ; Journal Article
ZDB-ID	2276646-7
ISSN	1681-7168 ; 1022-386X
ISSN (online)	1681-7168
ISSN	1022-386X
DOI	10.29271/jcpsp.2022.11.1441
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Article: Non-negative matrix factorization and differential expression analyses identify hub genes linked to progression and prognosis of glioblastoma multiforme

Akçay, Sevinç / Güven, Emine / Afzal, Muhammad / Kazmi, Imran

Gene. 2022 May 25, v. 824

2022

Abstract	One of the most prevailing primary brain tumors in adult human male is glioblastoma multiforme (GBM), which is categorized by rapid cellular growth. Even though the combination therapy comprises surgery, chemotherapy, and adjuvant therapies, the survival rate, on average, is 14.6 months. Glioma stem cells (GSCs) have key roles in tumorigenesis, progression, and defiance against chemotherapy and radiotherapy. In our study, firstly, the gene expression dataset GSE124145 was retrieved; the non-negative matrix factorization (NMF) method was applied on GBM dataset, and differentially expressed genes analysis (DEGs) was performed. After which, overlapping genes between metagenes and DEGs were detected to examine the Gene Ontology (GO) categories in the biological process (BP) in the stemness of GBM. The common hub genes were used to construct protein–protein interaction (PPI) network and further GO, while Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway was utilized to pinpoint the real hub genes. The analysis of hub genes particular for the same GO categories demonstrated that specific hub genes triggered distinct features of the same biological processes. After utilizing GSE124145 and The Cancer Genome Atlas (TCGA) dataset for survival analysis, we screened five real hub genes: GUCA1A, RFC2, GNG11, MMP19, and NRG1, which are strongly associated with the progression and prognosis of GBM. The DEGs analysis revealed that all real hub genes were overexpressed in GBM and TCGA datasets, which further validates our results. The constructed study of PPI, GO, and KEGG pathway on common hub genes was performed. Finally, the KEGG pathways performed on the top 15 candidate hub genes (including six real hub genes) of the PPI network in the GBM gene expression dataset study found mitogen-activated protein kinase (Mapk) signaling pathway to be the most significant pathway. The rest of the hub genes reviewed throughout the analysis might be favorable targets for diagnosing and treating GBM and lower-grade gliomas.
Keywords	adjuvants ; algorithms ; brain ; carcinogenesis ; cell growth ; data collection ; drug therapy ; gene expression regulation ; gene ontology ; genes ; glioblastoma ; males ; mitogen-activated protein kinase ; prognosis ; protein-protein interactions ; radiotherapy ; surgery ; survival rate
Language	English
Dates of publication	2022-0525
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	391792-7
ISSN	1879-0038 ; 0378-1119
ISSN (online)	1879-0038
ISSN	0378-1119
DOI	10.1016/j.gene.2022.146395
Database	NAL-Catalogue (AGRICOLA)

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Book ; Online: AUPIMO

Bertoldo, Joao P. C. / Ameln, Dick / Vaidya, Ashwin / Akçay, Samet

Redefining Visual Anomaly Detection Benchmarks with High Speed and Low Tolerance

2024

Abstract: Recent advances in visual anomaly detection research have seen AUROC and AUPRO scores on public benchmark datasets such as MVTec and VisA converge towards perfect recall, giving the impression that these benchmarks are near-solved. However, high AUROC ... ...

Abstract	Recent advances in visual anomaly detection research have seen AUROC and AUPRO scores on public benchmark datasets such as MVTec and VisA converge towards perfect recall, giving the impression that these benchmarks are near-solved. However, high AUROC and AUPRO scores do not always reflect qualitative performance, which limits the validity of these metrics in real-world applications. We argue that the artificial ceiling imposed by the lack of an adequate evaluation metric restrains progression of the field, and it is crucial that we revisit the evaluation metrics used to rate our algorithms. In response, we introduce Per-IMage Overlap (PIMO), a novel metric that addresses the shortcomings of AUROC and AUPRO. PIMO retains the recall-based nature of the existing metrics but introduces two distinctions: the assignment of curves (and respective area under the curve) is per-image, and its X-axis relies solely on normal images. Measuring recall per image simplifies instance score indexing and is more robust to noisy annotations. As we show, it also accelerates computation and enables the usage of statistical tests to compare models. By imposing low tolerance for false positives on normal images, PIMO provides an enhanced model validation procedure and highlights performance variations across datasets. Our experiments demonstrate that PIMO offers practical advantages and nuanced performance insights that redefine anomaly detection benchmarks -- notably challenging the perception that MVTec AD and VisA datasets have been solved by contemporary models. Available on GitHub: https://github.com/jpcbertoldo/aupimo.
Keywords	Computer Science - Computer Vision and Pattern Recognition
Subject code	006
Publishing date	2024-01-03
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: The efficacy of balance and proprioception exercises in female patients with knee osteoarthritis: A randomized controlled study.

Ince, Bugra / Goksel Karatepe, Altinay / Akcay, Seniz / Kaya, Taciser

Clinical rehabilitation

2022 Volume 37, Issue 1, Page(s) 60–71

Abstract: Objective: Loss of proprioception and balance disorders are commonly observed in patients with knee osteoarthritis. In this study, we aimed to investigate the effects of balance and proprioception exercises in patients with knee osteoarthritis.: ... ...

Abstract	Objective: Loss of proprioception and balance disorders are commonly observed in patients with knee osteoarthritis. In this study, we aimed to investigate the effects of balance and proprioception exercises in patients with knee osteoarthritis. Design: A single-center randomized trial with three parallel arms. Setting: A tertiary health care facility in Turkey. Participants: Female patients with knee osteoarthritis aged 40-70 years. Interventions: Ten-week exercise program in Biodex training, classical balance training and isometric strengthening groups. Main measures: Dynamic balance (overall stability index and the modified Clinical Test of Sensory Interaction and Balance), pain (visual analogue scale), physical function (30-s chair stand test and 40-meter fast-paced walk test) and quality of life (Knee Injury and Osteoarthritis Outcome Score). Results: Eighty-nine patients enrolled in the study. The Biodex training group, the classical training group, and the control group had overall stability index values of 1.0 ± 0.07, 1.4 ± 0.07 and 1.4 ± 0.07, and the Modified Clinical Test of Sensory Interaction and Balance - Condition-3 values of 0.7 ± 0.04, 0.9 ± 0.04 and 0.9 ± 0.04 respectively, at the end of treatment. In terms of pain scores on movement, each group showed significant improvement compared to their baseline, and the classical balance training group had better scores than the control group. No other significant difference was found between the groups. Physical function and quality of life outcomes showed significant main effects only in the time factor. Conclusions: Balance and proprioception exercises may have positive effects on dynamic balance and pain. The effects on physical function and quality of life should be investigated in further studies with larger sample.
MeSH term(s)	Humans ; Female ; Osteoarthritis, Knee ; Quality of Life ; Exercise Therapy ; Proprioception ; Pain ; Treatment Outcome
Language	English
Publishing date	2022-07-07
Publishing country	England
Document type	Randomized Controlled Trial ; Journal Article
ZDB-ID	639276-3
ISSN	1477-0873 ; 0269-2155
ISSN (online)	1477-0873
ISSN	0269-2155
DOI	10.1177/02692155221111929
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Article ; Online: Elevated serum fibrinogen/albumin ratios in patients with acute central serous chorioretinopathy.

Limon, Utku / Bozkurt, Erdinç / Bulut, Sinan / Ilkay, Betül / Akçay, Sezgin

European journal of ophthalmology

2022 Volume 32, Issue 3, Page(s) 1735–1742

Abstract: Purpose: To evaluate the serum fibrinogen/albumin ratios in patients with acute and chronic central serous chorioretinopathy, and healthy control samples.: Methods: Serum fibrinogen/albumin ratios were assessed in patients with acute (Group-1, 30 ... ...

Abstract	Purpose: To evaluate the serum fibrinogen/albumin ratios in patients with acute and chronic central serous chorioretinopathy, and healthy control samples. Methods: Serum fibrinogen/albumin ratios were assessed in patients with acute (Group-1, 30 eyes) and chronic (Group-2, 30 eyes) central serous chorioretinopathy, and compared with healthy control (Group-3, 30 eyes) samples. Results: Fibrinogen/albumin ratios were significantly higher in Group-1 (104.72 ± 12.34) than in Group-2 (75.83 ± 10.06) and in Group-3 (72 ± 9.54) ( Conclusion: The fibrinogen/albumin ratio may be useful as an inflammatory biomarker to monitor the systemic inflammatory state during the treatment and follow-up in patients with acute CSCR.
MeSH term(s)	Acute Disease ; Albumins ; Central Serous Chorioretinopathy/diagnosis ; Fibrinogen ; Fluorescein Angiography ; Humans ; Retrospective Studies ; Tomography, Optical Coherence ; Visual Acuity
Chemical Substances	Albumins ; Fibrinogen (9001-32-5)
Language	English
Publishing date	2022-03-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	1089461-5
ISSN	1724-6016 ; 1120-6721
ISSN (online)	1724-6016
ISSN	1120-6721
DOI	10.1177/11206721221089773
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Article ; Online: Analysis of the relationship between tuberculosis-related mortality and nitrous oxide emission levels in the world with the environmental Kuznets curve method.

Torun, Şerife / Yılmaz, Kadir / Özkaya, Şevket / Yosunkaya, Şebnem / Akçay, Şule

Turkish journal of medical sciences

2022 Volume 52, Issue 4, Page(s) 1329–1335

Abstract: Background: It was aimed to analyze the relationship between tuberculosis-related mortality and nitrous oxide emission levels in the world with the Environmental Kuznets Curve (EKC) Method.: Methods: WHO ICD-10 mortality list data and the World Bank ... ...

Abstract	Background: It was aimed to analyze the relationship between tuberculosis-related mortality and nitrous oxide emission levels in the world with the Environmental Kuznets Curve (EKC) Method. Methods: WHO ICD-10 mortality list data and the World Bank Country Data (WBCD) were used between 1997 and 2017 for 12 countries. Cubic regression analysis was used for EKC Analysis. Results: The difference between male and female deaths between 1996 and 1998 has increased sharply since 1999. Male deaths consistently occurred significantly more than female deaths. There was a significant and negative correlation between Nitrous oxide emissions (% change from 1990) and tuberculosis-related deaths, whereas there were significant and positive correlations between Nitrous oxide emissions in the energy sector (% of total) and tuberculosis-related deaths (p < 0.01). EKC analysis results showed that there is a U shaped between tuberculosis-related mortality and nitrous oxide emission levels in the world. Discussion: Research results show that the relationship between nitrous oxide change and mortality is negative in the short term and positive in the long term. Therefore, although nitrous oxide gases cause respiratory diseases and mortality, it may be possible to transform a harmful environmental factor into a positive by developing devices or methods that will convert these gases into free radicals.
MeSH term(s)	Female ; Male ; Humans ; Economic Development ; Nitrous Oxide ; Carbon Dioxide/analysis ; Tuberculosis
Chemical Substances	Nitrous Oxide (K50XQU1029) ; Carbon Dioxide (142M471B3J)
Language	English
Publishing date	2022-08-10
Publishing country	Turkey
Document type	Journal Article
ZDB-ID	1183461-4
ISSN	1303-6165 ; 1300-0144
ISSN (online)	1303-6165
ISSN	1300-0144
DOI	10.55730/1300-0144.5439
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Article ; Online: Can adipokines predict clinical prognosis and post-COVID lung sequelae?

Esendagli, Dorina / Topcu, Deniz / Gul, Eylem / Alperen, Cansu / Sezer, Rahime / Erol, Cigdem / Akcay, Sule

Respiratory investigation

2023 Volume 61, Issue 5, Page(s) 618–624

Abstract: Background: Adipokines play an important role in the regulation of inflammatory responses toward infections, including COVID-19. This study aimed to investigate the role of chemerin, adiponectin, and leptin in prognosis and post-COVID lung sequelae in ... ...

Abstract	Background: Adipokines play an important role in the regulation of inflammatory responses toward infections, including COVID-19. This study aimed to investigate the role of chemerin, adiponectin, and leptin in prognosis and post-COVID lung sequelae in hospitalized patients with COVID-19. Methods: Serum levels of the three adipokines were measured upon admission of polymerase chain reaction-confirmed patients with COVID-19 who were followed up for 6 months for the clinical outcome and lung sequelae formation. Results: A total of 77 patients were included in the study. Of the 77 patients, 58.4% were males, and the median age was 63.2 ± 18.3 years. Fifty-one patients (66.2%) had a good prognosis. Among adipokines, only chemerin was significantly lower in the bad prognosis group (P < 0.05), and the serum levels showed a negative correlation with age (rho = -0.238; P < 0.05). Leptin levels were negatively correlated with gamma glutamyl transferase levels, which were significantly higher in the bad prognostic group (rho = -0.240; P < 0.05). Twenty-four patients had no lung sequelae, and 20 developed sequelae within 6 months after infection. Chemerin/adiponectin ratio with a cut-off value of 0.96 and an area under the curve 0.679 (P < 0.05) might predict the sequelae formation. Conclusions: Chemerin levels are lower, especially in patients with a bad prognosis, and the chemerin/adiponectin ratio might predict the development of lung sequelae in patients with COVID-19.
MeSH term(s)	Male ; Humans ; Adult ; Middle Aged ; Aged ; Aged, 80 and over ; Female ; Adipokines ; Leptin ; Adiponectin ; COVID-19/complications ; Prognosis ; Disease Progression
Chemical Substances	Adipokines ; Leptin ; Adiponectin
Language	English
Publishing date	2023-07-09
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	2660821-2
ISSN	2212-5353 ; 2212-5345
ISSN (online)	2212-5353
ISSN	2212-5345
DOI	10.1016/j.resinv.2023.06.001
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