Publications by authors named "Omer Yılmaz"

Background: Antenatal hydronephrosis (ANH) is one of the most common abnormalities detected during prenatal ultrasound. There is significant variability in the postnatal management of ANH. Our objective was to report the outcomes of patients with ANH, spontaneous resolution rates, surgical intervention rates, and factors contributing to these parameters.

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Modulation of immune tone at mucosal surfaces is critical to maintain homeostasis while facilitating the handling of emerging threats. One dynamic component of immune modulation is the phagocytosis and clearance of apoptotic bodies known as efferocytosis that inhibits inflammation by promoting its resolution. Here, we evaluated the effects of apoptotic body phagocytosis by intestinal epithelial stem and progenitor cells (ISCs).

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Recently, a GuMI gut microphysiological system has been established to coculture oxygen-intolerant () A2-165 with organoids-derived primary human colonic epithelium. This study aims to test if this GuMI system applies to different donors with different healthy states and uses metabolomics to reveal the role of gut microbes in modulating host- and diet-derived molecules in the gut lumen. Organoids-derived colonic monolayers were generated from an uninflamed region of diverticulitis, ulcerative colitis, and Crohn's disease patients and then integrated into the GuMI system to coculture with A2-165 for 2 to 4 days.

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  • 5-fluorouracil (5-FU) is an important cancer treatment that mostly works by blocking a specific enzyme, leading to DNA damage, but clinical trials show it doesn't work well with certain other drugs for colorectal cancer.
  • Research indicates that 5-FU actually kills colorectal cancer cells by targeting RNA during the process of making ribosomes, rather than mainly causing DNA damage, which some cancer types are more sensitive to.
  • Strategies that increase ribosome production may enhance the effectiveness of 5-FU, suggesting that combining treatments that focus on this aspect could improve outcomes in cancer therapy.
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  • Data-Independent Acquisition (DIA) enhances co-immunoprecipitation analysis by reducing quantitation variability and improving the detection of specific interactors compared to Data-Dependent Acquisition (DDA).
  • A comparison of DIA and DDA across various bioinformatics workflows revealed that DIA can effectively generate spectral libraries without needing separate DDA experiments, and software struggles with indistinct signals from mock pull-downs.
  • Spectronaut and DIA-NN provided the best control of coefficient of variation in protein quantification, while using DIA for both building spectral libraries and quantifying proteins leads to more consistent results and fewer missing values.
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  • * The gastrointestinal tract, crucial for nutrient absorption, is continuously renewed and affected by diet, with intestinal stem cells playing a key role in maintaining this balance and being responsive to diet and metabolic changes.
  • * The review examines how various diets and metabolic shifts affect intestinal stem cells, tumor growth, and the intestinal epithelium in both normal and disease states, highlighting the intricate relationship between diet and health outcomes.
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Polyamines are abundant and evolutionarily conserved metabolites that are essential for life. Dietary polyamine supplementation extends life-span and health-span. Dysregulation of polyamine homeostasis is linked to Parkinson's disease and cancer, driving interest in therapeutically targeting this pathway.

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Background: The effects of trabeculectomy on anterior segment parameters have been widely investigated. However, the stabilization time for various glaucoma types after trabeculectomy remains debatable. We investigated the effect of mitomycin C-augmented trabeculectomy on ocular anterior segment parameters in primary open-angle glaucoma (POAG) and pseudoexfoliation glaucoma (PXG) during short-term follow-up using the Pentacam HR.

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  • Fasting has been shown to enhance health, lifespan, and tissue repair across various organisms, including humans, but the impact of post-fast refeeding on adult stem cells and cancer development is not well understood.
  • Research indicates that refeeding after fasting boosts intestinal stem cell growth and increases the risk of tumors, especially when the tumor suppressor gene Apc is absent in the stem cells.
  • The study's findings highlight the activation of mTORC1 in post-fast-refed stem cells, which promotes protein synthesis and regeneration, suggesting that diet strategies should carefully manage refeeding to avoid raising cancer risks.
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  • Metastases originate from specific subsets of cancer cells that spread from the primary tumor, with their ability to thrive in new locations being impacted by genetic and epigenetic changes.
  • Certain types of cancers tend to consistently metastasize to particular tissues, indicating that the characteristics of the primary tumor play a role in determining metastatic sites.
  • Research shows that both primary and metastatic pancreatic tumors share metabolic traits and that cancer cells prefer to grow in their original site rather than in new metastatic locations, highlighting the influence of the tumor's tissue of origin on its growth and spread.
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Animal studies are needed that best simulate a large-scale, inhomogeneous body exposure after a radiological or nuclear incident and that provides a platform for future development of medical countermeasures. A partial-body irradiation (PBI) model using 137Cs gamma rays with hind limb (tibia) shielding was developed and assessed for the sequalae of radiation injuries to gastrointestinal tract, bone marrow (BM) and lung and among different genetic mouse strains (C57BL/6J, C57L/J, CBA/J and FVB/NJ). In this case, a marginal level of BM shielding (∼2%) provided adequate protection against lethality from infection and hemorrhage and enabled escalation of radiation doses with evaluation of both acute and delayed radiation syndromes.

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Background & Aims: Single-cell RNA sequencing (scRNA) has empowered many insights into gastrointestinal microenvironments. However, profiling human biopsies using droplet-based scRNA (D-scRNA) is challenging since it requires immediate processing to minimize epithelial cell damage. In contrast, picowell-based (P-scRNA) platforms permit short-term frozen storage before sequencing.

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The study aimed to investigate Candida albicans presence, antifungal resistance, biofilm formation, putative virulence genes, and molecular characterization in oral samples of dogs and cats. A total of 239 oral samples were collected from cats and dogs of various breeds and ages at Erciyes University, Faculty of Veterinary Medicine Clinics, between May 2017 and April 2018. Among 216 isolates obtained, 15 (6.

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Purpose: Evaluation of anterior segment parameters using the Scheimpflug corneal topography 1 year after surgery in patients who underwent sutureless scleral fixation intraocular lens (SFIOL) implantation using the modified Yamane technique and retropupillary iris-claw intraocular lens (RPIOL) implantation.

Methods: A total of 60 eyes from 57 patients who underwent sutureless SFIOL implantation and 57 eyes from 52 patients who underwent RPIOL implantation were included. Anterior chamber depth (ACD), anterior chamber angle (ACA), anterior chamber volume (ACV), anterior-posterior corneal astigmatism, and keratometric values were assessed using the Scheimpflug corneal topography (Pentacam HR, Germany).

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  • Researchers studied how certain proteins in colorectal cancer could affect how the immune system interacts with tumors and the outcomes for patients.
  • They looked at a lot of tumor samples and found that tumors with low levels of a protein called B2M were often more aggressive and missed important immune markers.
  • The results show that measuring B2M can help predict how well patients might respond to treatments and understand their survival chances.
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  • Some doctors use a special stain called elastin to check for something called venous invasion (VI) in patients with colorectal cancer, as it can change how they treat the disease.
  • The study divided patients into two groups: one got one elastin stain, and the other got multiple stains. It found that using multiple stains helped find VI more often, especially in advanced stages of cancer.
  • However, using more than two stains didn’t really make a difference in predicting how well patients would do, so the researchers suggest sticking to using two stains for better results without going overboard.
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Background: Bell's phenomenon, also known as the palpebral oculogyric reflex, is a critical reflex that protects the cornea. We developed an innovative, simple, and practical grading scale for Bell's phenomenon that includes the inverse Bell's phenomenon. Using this scale, we investigated the characteristics of Bell's phenomenon among asymptomatic individuals in different age groups and examined the frequency of ocular surface lesions in asymptomatic and symptomatic participants with different grades.

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A hallmark of cancer is the avoidance of immune destruction. This process has been primarily investigated in locally advanced or metastatic cancer; however, much less is known about how pre-malignant or early invasive tumours evade immune detection. Here, to understand this process in early colorectal cancers (CRCs), we investigated how naive colon cancer organoids that were engineered in vitro to harbour Apc-null, Kras and Trp53-null (AKP) mutations adapted to the in vivo native colonic environment.

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Different gut microbial metabolites have the potential to promote and protect against colorectal cancer (CRC). A study now links -3-indoleacrylic acid (IDA), a metabolite derived from , with colorectal carcinogenesis through a distinct ferroptosis pathway AHR–ALDH1A3–FSP1–CoQ.

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Deregulation of cellular metabolism has recently emerged as a notable cancer characteristic. This reprogramming of key metabolic pathways supports tumor growth. Targeting cancer metabolism demonstrates the potential for managing colorectal cancer.

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Under chronic stress, cells must balance competing demands between cellular survival and tissue function. In metabolic dysfunction-associated steatotic liver disease (MASLD, formerly NAFLD/NASH), hepatocytes cooperate with structural and immune cells to perform crucial metabolic, synthetic, and detoxification functions despite nutrient imbalances. While prior work has emphasized stress-induced drivers of cell death, the dynamic adaptations of surviving cells and their functional repercussions remain unclear.

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