Identification of piRNA Binding Sites Reveals the Argonaute Regulatory Landscape of the C. elegans Germline.

piRNAs (Piwi-interacting small RNAs) engage Piwi Argonautes to silence transposons and promote fertility in animal germlines. Genetic and computational studies have suggested that C. elegans piRNAs tolerate mismatched pairing and in principle could target every transcript. Here we employ in vivo cross-linking to identify transcriptome-wide interactions between piRNAs and target RNAs. We show that piRNAs engage all germline mRNAs and that piRNA binding follows microRNA-like pairing rules. Targeting correlates better with binding energy than with piRNA abundance, suggesting that piRNA concentration does not limit targeting. In mRNAs silenced by piRNAs, secondary small RNAs accumulate at the center and ends of piRNA binding sites. In germline-expressed mRNAs, however, targeting by the CSR-1 Argonaute correlates with reduced piRNA binding density and suppression of piRNA-associated secondary small RNAs. Our findings reveal physiologically important and nuanced regulation of individual piRNA targets and provide evidence for a comprehensive post-transcriptional regulatory step in germline gene expression.

ZNFX-1 Functions within Perinuclear Nuage to Balance Epigenetic Signals.

Animal cells have a remarkable capacity to adopt durable and heritable gene expression programs or epigenetic states that define the physical properties and diversity of somatic cell types. The maintenance of epigenetic programs depends on poorly understood pathways that prevent gain or loss of inherited signals. In the germline, epigenetic factors are enriched in liquid-like perinuclear condensates called nuage. Here, we identify the deeply conserved helicase-domain protein, ZNFX-1, as an epigenetic regulator and component of nuage that interacts with Argonaute systems to balance epigenetic inheritance. Our findings suggest that ZNFX-1 promotes the 3' recruitment of machinery that propagates the small RNA epigenetic signal and thus counteracts a tendency for Argonaute targeting to shift 5' along the mRNA. These functional insights support the idea that recently identified subdomains of nuage, including ZNFX-1 granules or "Z-granules," may define spatial and temporal zones of molecular activity during epigenetic regulation.

Efficacy of cumulative cisplatin dose on survival in patients with locally advanced cervical cancer treated with definitive chemoradiotherapy: multicenter study by Turkish Oncology Group.

OBJECTIVE: To investigate the impact of cumulative cisplatin dose on clinical outcomes in locally advanced cervical cancer patients undergoing definitive chemoradiotherapy. METHODS: A retrospective analysis was conducted on 654 patients with stage IB3-IVA disease treated with definitive chemoradiotherapy. Radiotherapy was applied as external beam pelvic with or without para-aortic radiotherapy and brachytherapy. Concomitant chemotherapy was in the form of weekly or 3 weekly cisplatin. Data on demographics, treatment protocols, cumulative cisplatin dose, adverse effects, and survival outcomes were collected. Statistical analyses, including univariate and multivariate Cox regression models, were used to assess factors influencing progression free survival and overall survival. RESULTS: The median cumulative cisplatin dose was 210 mg (range 40-320), and ≥200 mg in 503 (76.9%) patients. Median follow-up was 35 months (range 1-150). The 5 year progression free survival and overall survival rates were 66.9% and 77.1%, respectively. Multivariate analysis identified poor performance status, non-squamous cell histology, presence of lymph node metastases, and hemoglobin <10 g/dL before chemoradiotherapy as poor prognostic factors for both progression free survival and overall survival in the whole group. When stage III cases were evaluated separately, the cumulative cisplatin dose <200 mg was found to be a significant poor prognostic factor in overall survival (hazard ratio 1.79, 95% confidence interval 1.1 to 3.0, p=0.031). CONCLUSION: Our study showed that a cumulative cisplatin dose >200 mg, particularly in patients with lymph node metastases, significantly improved overall survival. Factors such as anemia, toxicity related challenges, and comorbidities were identified as critical considerations in treatment planning. These findings emphasize the balance between maximizing therapeutic efficacy and managing toxicity, guiding personalized treatment approaches for locally advanced cervical cancer.

Comparative analysis of ChatGPT, Gemini and emergency medicine specialist in ESI triage assessment.

INTRODUCTION: The term Artificial Intelligence (AI) was first coined in the 1960s and has made significant progress up to the present day. During this period, numerous AI applications have been developed. GPT-4 and Gemini are two of the best-known of these AI models. As a triage system The Emergency Severity Index (ESI) is currently one of the most commonly used for effective patient triage in the emergency department. The aim of this study is to evaluate the performance of GPT-4, Gemini, and emergency medicine specialists in ESI triage against each other; furthermore, it aims to contribute to the literature on the usability of these AI programs in emergency department triage. METHODS: Our study was conducted between February 1, 2024, and February 29, 2024, among emergency medicine specialists in Turkey, as well as with GPT-4 and Gemini. Ten emergency medicine specialists were included in our study but as a limitation the emergency medicine specialists participating in the study do not frequently use the ESI triage model in daily practice. In the first phase of our study, 100 case examples related to adult or trauma patients were extracted from the sample and training cases found in the ESI Implementation Handbook. In the second phase of our study, the provided responses were categorized into three groups: correct triage, over-triage, and under-triage. In the third phase of our study, the questions were categorized according to the correct triage responses. RESULTS: In the results of our study, a statistically significant difference was found between the three groups in terms of correct triage, over-triage, and under-triage (p < 0.001). GPT-4 was found to have the highest correct triage rate with an average of 70.60 (±3.74), while Gemini had the highest over-triage rate with an average of 35.2 (±2.93) (p < 0.001). The highest under-triage rate was observed in emergency medicine specialists (32.90 (±11.83)). In the ESI 1-2 class, Gemini had a correct triage rate of 87.77%, GPT-4 had 85.11%, and emergency medicine specialists had 49.33%. CONCLUSION: In conclusion, our study shows that both GPT-4 and Gemini can accurately triage critical and urgent patients in ESI 1&2 groups at a high rate. Furthermore, GPT-4 has been more successful in ESI triage for all patients. These results suggest that GPT-4 and Gemini could assist in accurate ESI triage of patients in emergency departments.

Comparison of emergency medicine specialist, cardiologist, and chat-GPT in electrocardiography assessment.

INTRODUCTION: ChatGPT, developed by OpenAI, represents the cutting-edge in its field with its latest model, GPT-4. Extensive research is currently being conducted in various domains, including cardiovascular diseases, using ChatGPT. Nevertheless, there is a lack of studies addressing the proficiency of GPT-4 in diagnosing conditions based on Electrocardiography (ECG) data. The goal of this study is to evaluate the diagnostic accuracy of GPT-4 when provided with ECG data, and to compare its performance with that of emergency medicine specialists and cardiologists. METHODS: This study has received approval from the Clinical Research Ethics Committee of Hitit University Medical Faculty on August 21, 2023 (decision no: 2023-91). Drawing on cases from the "150 ECG Cases" book, a total of 40 ECG cases were crafted into multiple-choice questions (comprising 20 everyday and 20 more challenging ECG questions). The participant pool included 12 emergency medicine specialists and 12 cardiology specialists. GPT-4 was administered the questions in a total of 12 separate sessions. The responses from the cardiology physicians, emergency medicine physicians, and GPT-4 were evaluated separately for each of the three groups. RESULTS: In the everyday ECG questions, GPT-4 demonstrated superior performance compared to both the emergency medicine specialists and the cardiology specialists (p < 0.001, p = 0.001). In the more challenging ECG questions, while Chat-GPT outperformed the emergency medicine specialists (p < 0.001), no significant statistical difference was found between Chat-GPT and the cardiology specialists (p = 0.190). Upon examining the accuracy of the total ECG questions, Chat-GPT was found to be more successful compared to both the Emergency Medicine Specialists and the cardiologists (p < 0.001, p = 0.001). CONCLUSION: Our study has shown that GPT-4 is more successful than emergency medicine specialists in evaluating both everyday and more challenging ECG questions. It performed better compared to cardiologists on everyday questions, but its performance aligned closely with that of the cardiologists as the difficulty of the questions increased.

Effect of tumor-infiltrating immune cells (mast cells, neutrophils and lymphocytes) on neoadjuvant chemotherapy response in breast carcinomas.

INTRODUCTION: Despite screening, the incidence of breast cancer is increasing worldwide. Neoadjuvant chemotherapy (NAC) response is one of the most important parameters taken into consideration in surgery, optimal adjuvant chemotherapy planning and prognosis prediction. Research on predictive markers for the response to NAC is still ongoing. In our study, we investigated the relationship between tumor-infiltrating neutrophils/mast cells/lymphocytes and NAC response in breast carcinomas. MATERIAL AND METHOD: Study included 117 patients who were diagnosed with invasive breast carcinoma using core needle biopsy. In these biopsies tumor-infiltrating neutrophils/mast cells/lymphocytes were evaluated and Miller Payne Score was used for NAC response. RESULT: 53 patients exhibited high TILs, 36 had high TINs, and 46 showed high TIMs. While pathological complete response was 27 % in all patients, it was 38 % in high TINs patients, 35 % in high TILs patients, and 28 % in high TIMs patients. High TIMs were observed to be statistically associated with survival. TILs, TINs, nuclear grade, ER, PR and HER2 expression, Ki-67 proliferation index were found to be associated with the Miller - Payne score. In multivariate analysis, TINs, nuclear grade, pathological stage, and molecular subtype were found to be independent risk factors for treatment response. CONCLUSION: TINs have better prognostic value to predict neoadjuvant treatment than TILs. High TIMs are associated with increased overall survival. The inclusion of TINs in NAC response and TIMs in overall survival in pathology reports and treatment planning is promising in breast carcinomas as they are simple to use and reproducible markers.

The anti-scar effect of tyrosine-kinase inhibitor nintedanib in experimental glaucoma filtration surgery in rabbits.

PURPOSE: To investigate the efficacy of nintedanib on preventing postoperative scar in formation following glaucoma filtering surgery (GFC) in rabbits in comparison with Mitomycin-C (MMC). DESIGN: Experimental Animal Study. METHODS: 24 New Zealand rabbits were divided randomly into 3 groups as Sham, Nindetanib and MMC(n = 8). Limbal-based trabeculectomy was performed on the right eyes of the rabbits. Left eyes that did'nt undergo surgery were included in the control group (n = 8). Following surgery, Intraocular pressures (IOP), postoperative complications and morphological changes in the bleb were evaluated. On the 28th day, eight eyes from each group were enucleated and histologically and immunohistochemically analyzed. Matrix metalloproteinase-2 (MMP-2), Transforming Growth Factor-1 (TGF-B1) and alpha-smooth muscle actin (a-SMA) were evaluated. RESULTS: It was observed that nintedanib has no side effects and reduces subconjunctival fibrosis. Postoperative IOP values in the Nindetanib group were lower than the other groups (p < 0.05). The longest bleb survival was observed in the Nintedanib group and the shortest in the Sham group (p < 0.001). Conjunctival vascularity and inflammation was reduced in the Nintedanib group compared to the Sham group (p < 0.05). The highest subconjunctival fibrosis was observed in the Sham group and the least in the Nintedanib group (p < 0.05). Although the fibrosis score was found lower in the Nintedanib group compared to the MMC(p > 0.05). α-SMA TGF-ß1, MMP-2 expressions were similar in Nintedanib and MMC groups (p > 0.05), however, it was observed that significantly decreased in both groups compared to Sham group (p < 0.05). CONCLUSION: It has been observed that Nindetanib suppress fibroblast proliferation Thus, It may be a drug that can prevent subconjunctival fibrosis in GFC.

Prognostic Value of Inflammation And Nutrition-Based Scores in Non-Small Cell Lung Cancer.

OBJECTIVE: In studies conducted on non-small cell lung cancer (NSCLC) patients, many factors such as age, stage, weight loss, lymph node, and pleural involvement have been shown to affect survival. On the other hand, systemic inflammation plays a critical role in proliferation, migration, invasion, and metastasis. Inflammation and nutrition-based prognostic scores are reported to be associated with survival in patients with NSCLC. The aim of our study is to show the effects of these scores on survival and disease progression in NSCLC patients. SUBJECTS AND METHODS: Neutrophil to lymphocyte ratio (NLR), platelet to lymphocyte ratio (PLR), modified Glasgow prognostic score (mGPS), and prognostic nutritional index (PNI) values in 102 patients with stage 1,2 and 3A NSCLC were analyzed retrospectively. RESULTS: NLR (p < 0.001), PLR (p = 0.001), PNI (p < 0.001), and mGPS (p = 0.001) variables showed a statistically significant difference according to mortality groups. NLR and PLR values were higher in exitus patients. However, PNI values were higher in surviving patients. NLR (p < 0.001), PLR (p = 0.004), PNI (p = 0.001), and mGPS (p = 0.015) variables showed a statistically significant difference in terms of locoregional recurrence. PNI (p = 0.001) and mGPS (p = 0.001) in terms of distant metastasis development during follow-up and treatment, showed a statistically significant difference. CONCLUSION: NLR, PLR, PNI, and mGPS are easily accessible and non-invasive parameters and provide predictive information about survival and disease course. We showed the effect of these parameters on the prognosis.

The therapeutical effects of damage-specific stress induced exosomes on the cisplatin nephrotoxicity IN VIVO.

Cisplatin is one of the metal containing drugs for the solid cancer treatments. However, its side-effects limit its application in the cancer treatment. Stem cell therapy is a promising treatment for the tissue damage caused by the chemotherapeutic agents, like cisplatin. Exosomes secreted by mesenchymal stem cells (MSCs) could be used for cell-free regenerative treatment, but their potency and reproducibility are questionable. In this study, the microenvironment of the renal tubular epithelial cells was mimicked by coculture of endothelial-, renal proximal tubule epithelial- and fibroblast cells. Cisplatin was applied to this tricell culture model, and the secreted rescue signals were collected and used to induce MSCs. From these stress-induced MSCs, the (stress-induced) exosomes were collected and used for the cell-free therapeutic treatment of cisplatin-treated rats with acute kidney injury. The composition of the stress-induces exosomes was compared with the non-induced exosomes and found that the expression of some critical factors for cell proliferation, repair mechanism and oxidative stress was improved. The cisplatin-damaged renal tissue showed substantial recovery after the treatment with stress-induced exosomes compared to the treatment with non-induced exosomes. Although, the non-induced exosomes showed their activity mostly as cytoprotective, the induced exosomes further involved actively in the tissue regeneration, like MSCs. It was shown that the exosomes could be reprogrammed to improve their therapeutic effect to be used in cell-free regenerative medicine. Further, cisplatin-induced tissue damage in the kidney might be effectively prevented and used for tissue regeneration by use of induced exosomes generated for a particular damage.

Children's Perioperative Multidimensional Anxiety Scale (CPMAS): Turkish Validity and Reliability Study.

PURPOSE: To test the validity and reliability of the Turkish version of the Children's Perioperative Multidimensional Anxiety Scale (CPMAS). DESIGN: Methodological research model. METHODS: One hundred children (81% male) aged 7 to 13 years undergoing elective surgery at a tertiary university hospital were included. Self-administered CPMAS and State-Trait Anxiety Inventory-Children were used to collect data at preoperative, operation day, and a month after the operation. Internal consistency, test-retest reliability, parallel form reliability, and content and construct validity of the tools were determined across all three visits. FINDINGS: The CPMAS demonstrated good test-retest reliability (ICC = 0.51 to 0.78) and good internal consistency (Cronbach's alpha = 0.78 to 0.81). Inter item correlation values were ranged from 0.20 to 0.62 at preoperative, 0.32 to 0.64 on the day of operation and 0.36 to 0.75 at a month after the operation. CPMAS single-factor construct and the explanatory percentages were 0.54 and above. After Pearson correlation analysis, CPMAS was moderately correlated with State-Trait Anxiety Inventory-Children at T1 (r = 0.54, P < .01) and T2 (r = 0.56, P < .01). CONCLUSIONS: The Turkish version of CPMAS has good reliability and validity score. Therefore, it is a suitable instrument to assess perioperative anxiety in 7 to 13 years old children in a clinical setting.

Protective effects of citicoline-containing eye drops against UVB-Induced corneal oxidative damage in a rat model.

It has been reported that citicoline increases antioxidant activity in some tissues. However, the effect of citicoline on corneal wound-healing has not yet been demonstrated. The aim was to investigate the protective effects of citicoline on ultraviolet B (UVB) radiation-induced corneal oxidative damage in a rat model. Four groups (eight animals each) were investigated: controls; UVB only; UVB/citicoline; and citicoline only. Corneal oxidative damage was induced by exposure to UVB radiation at 560 µW/cm2 for five days in the UVB-exposed groups and 1% citicoline eye drops were applied (3xday) for eight days in the two citicoline groups. Corneal surface damage was evaluated by opacity and fluorescein staining. Corneal injury was assessed biochemically by measuring the concentrations of glutathione (GSH) and malondialdehyde (MDA) and the activity of corneal superoxide dismutase (SOD) and catalase. Matrix metalloproteinase (MMP) -2 and -9 and caspase-3 were evaluated by immunofluorescent staining and microscopic examination and by Western blot analysis. Corneal gene expression analysis was performed for vascular endothelial growth factor (VEGF), interleukin-1 beta (IL-1ß) and transforming growth factor-beta (TGF-ß). UVB radiation caused significant epithelial damage and evident opacity in the cornea, together with a local decrease in SOD, catalase and GSH activity. Corneal MDA concentrations increased with UVB exposure. The UVB/Citicoline group had significantly less corneal damage, greater SOD, catalase and GSH activity, and decreased MDA concentrations compared to the UVB only group (p < 0.05). Expression of TGF-ß, IL-1ß and VEGF was significantly lower in the citicoline/UVB group compared to the UVB group (p < 0.05). Interestingly, TGF-ß expression was lower in the citicoline only group compared with controls. Immunfluorescent staining and Western blot analysis showed increased MMP-2, -9 and caspase-3 in the UVB only group compared with the UVB/citicoline group. It was shown that citicoline treatment may be effective in suppressing oxidative stress and controlling inflammation in UVB corneal injury.

Anxiety levels of breast cancer patients in Turkey during the COVID-19 pandemic.

Aim: To assess the anxiety levels of breast cancer patients during the COVID-19 pandemic. Materials & methods: A total of 298 patients completed the State-Trait Anxiety Inventory (STAI-S and STAI-T) and the Visual Analogue Scale for Anxiety (VAS) and VAS for Anxiety in COVID-19 (VAS-CoV). Results: 144 patients were in the high anxiety category for STAI-S, and 202 patients were in the high anxiety category for STAI-T. STAI-T score was significantly high in the metastatic group (p = 0.017). VAS-CoV score in the hormonotherapy group was significantly higher than in the no-treatment group (p = 0.023). There was a positive correlation between VAS-CoV and VAS levels (r = 0.708, p < 0.001), VAS-CoV and STAI-S and STAI-T scores (r = 0.402, p < 0.001; r = 0.185, p = 0.001, respectively), and a negative correlation between education years and STAI-T scores (r = -0.172, p = 0.003). Conclusion: The COVID-19 pandemic is related to high anxiety levels in breast cancer patients.

Lay abstract COVID-19 pandemic is related to rapidly rising anxiety levels worldwide. Because of the high mortality of COVID-19 in cancer patients, changing treatment routines and disruptions of the healthcare system, cancer patients are the most affected population in this situation. Anxiety among females and breast cancer patients tend to be high, although anxiety levels in cancer patients during the pandemic period varies according to the cancer type, treatment status and sociodemographic factors. This study assessed the effect of the COVID-19 pandemic on breast cancer patients' anxiety levels according to treatment status and stage of the disease. A total of 298 breast cancer patients completed the universally validated anxiety questionnaires. Results demonstrated high trait anxiety in breast cancer patients, particularly in the metastatic group. The current findings highlighted the importance of intensive assessment and close monitoring of breast cancer patients' psychological situations. It is crucial to provide psychological support to breast cancer patients to contribute to both treatment and follow-up processes during the pandemic.

The effect of demographic, clinical, and pathological data on quality of life in rectum cancer.

PURPOSE: The aims of the current study are to describe the quality of life among patients with rectal cancer and to determine the clinical and demographic correlation that influences the quality of life of rectal cancer patients. METHOD: In this study, 50 patients with rectal cancer treated in the Radiation Oncology Department of Kayseri City Education and Research Hospital were included. Ethics committee approval was received for the study. Data collection form was used to determine the demographic and clinicopathological characteristics of the patients. To assess the quality of life, the European Committee of Cancer Treatment and Organization Quality of Life Scale (EORTC QLQ-C30) question-answer scale was used. The data were collected by interviewing the patients face to face. Mann-Whitney U and Kruskal-Wallis tests were used to analyze the data. Spearman correlation analysis was performed to reveal the relationship between dependent variables. RESULTS: As a result of this study, 52% of patients were 65 years and older and 54% were male patients. The most common surgery was low anterior resection and the most common type of pathology was adenocarcinoma. According to American Cancer Committee (AJCC) 7th edition 2009 staging, 80% stage 3 was the most common. In EORTC C30 Cancer Quality of Life Scale Functional Scale Subscale, the highest score is from the physical function and the lowest score is from the emotional function. In the symptom scale subscale, the most common symptom was nausea/vomiting. Performance status (ECOG) was found to be significantly associated with T stage, N stage, TNM stage, and symptom scores. There was a moderately significant positive correlation between symptom scales and global health status scales (ρ = 0.51; p < 0.001). There was a perfectly positive and significant relationship between symptom scales and functional scales (ρ = 0.83; p < 0.001). CONCLUSIONS: As a result of this study we conducted, it was observed that rectal cancer patients decreased performance status and increased symptoms in the presence of advanced disease. Accordingly, it was found that the quality of life of the patient decreased.

Four-site skinfolds thickness percentiles of schoolchildren and adolescents in Turkey.

OBJECTIVE: The primary purpose of the current study was to establish Turkish smoothed centile charts and Lambda, Mu, Sigma (LMS) tables for four-site skinfold thickness based on a population-based sample, and secondary purpose was to elaborate a reference for the percentage of body fat. DESIGN: A cross-sectional and descriptive study was conducted between January and May 2017. Triceps, biceps and subscapular, suprailiac skinfold thicknesses were measured using Holtain skinfold caliper. Age- and gender-specific percentile values were determined with the LMS method, and body fat percentage was calculated using the Westrate and Deurenberg equation. SETTING: Afyonkarahisar province in Turkey. PARTICIPANTS: The current study was conducted on 4565, 6-18-year-old students. RESULTS: The triceps, biceps and subscapular skinfolds of the girls were higher than the boys. From the age of seven, the sum of four skinfold thicknesses of the girls was more than those of the boys. This difference became more evident after the age of 12. Although fat percentages of girls showed a fluctuating change, it decreased with the age in boys. Westrate and Deurenberg equation fat percentages of girls until adolescence were lower than boys, but increased after 12 years of age and exceeded that of boys. CONCLUSIONS: The current study has provided sex- and age-specific reference values for skinfold thickness and has shown that obesity in girls is higher than in boys in schoolchildren in Afyonkarahisar. The current study has also shown that skinfold thickness measurements are a valuable tool for screening obesity in children.

DolphinNext: a distributed data processing platform for high throughput genomics.

BACKGROUND: The emergence of high throughput technologies that produce vast amounts of genomic data, such as next-generation sequencing (NGS) is transforming biological research. The dramatic increase in the volume of data, the variety and continuous change of data processing tools, algorithms and databases make analysis the main bottleneck for scientific discovery. The processing of high throughput datasets typically involves many different computational programs, each of which performs a specific step in a pipeline. Given the wide range of applications and organizational infrastructures, there is a great need for highly parallel, flexible, portable, and reproducible data processing frameworks. Several platforms currently exist for the design and execution of complex pipelines. Unfortunately, current platforms lack the necessary combination of parallelism, portability, flexibility and/or reproducibility that are required by the current research environment. To address these shortcomings, workflow frameworks that provide a platform to develop and share portable pipelines have recently arisen. We complement these new platforms by providing a graphical user interface to create, maintain, and execute complex pipelines. Such a platform will simplify robust and reproducible workflow creation for non-technical users as well as provide a robust platform to maintain pipelines for large organizations. RESULTS: To simplify development, maintenance, and execution of complex pipelines we created DolphinNext. DolphinNext facilitates building and deployment of complex pipelines using a modular approach implemented in a graphical interface that relies on the powerful Nextflow workflow framework by providing 1. A drag and drop user interface that visualizes pipelines and allows users to create pipelines without familiarity in underlying programming languages. 2. Modules to execute and monitor pipelines in distributed computing environments such as high-performance clusters and/or cloud 3. Reproducible pipelines with version tracking and stand-alone versions that can be run independently. 4. Modular process design with process revisioning support to increase reusability and pipeline development efficiency. 5. Pipeline sharing with GitHub and automated testing 6. Extensive reports with R-markdown and shiny support for interactive data visualization and analysis. CONCLUSION: DolphinNext is a flexible, intuitive, web-based data processing and analysis platform that enables creating, deploying, sharing, and executing complex Nextflow pipelines with extensive revisioning and interactive reporting to enhance reproducible results.

Anatomy of the Anterior Clinoid Process in Human Fetuses.

PURPOSE: The main objective of this study was to display the morphologic properties of the anterior clinoid process (ACP) in human fetuses in term of early childhood surgeries. METHODS: Twenty-four (10 females and 14 males) fetal cadavers aged from 16th to 28th weeks of gestation (at mean, 21.54 ±â€Š3.11 weeks) were included in the present study. The dimensions of ACP were measured with a digital image analysis software. RESULTS: Taking into account the length, width, and angle of ACP, it was classified as Type 1 in 20.83% (10 cases), Type 2 in 10.42% (5 cases), Type 3 in 10.42% (5 cases), Type 4 in 2.08% (1 case), Type 5 in 8.33% (4 cases), Type 6 in 16.67% (8 cases), Type 7 in 8.33% (4 cases), and Type 8 in 22.92% (11 cases). According to the attachment site of the optic strut (OS) relative to ACP, OS was identified as the anterior 3/5 in 16.67% (8 cases), anterior 4/5 in 68.75% (33 cases), and posterior 1/5 in 14.58% (7 cases). Neither right-left nor male-female significant differences were observed between the quantitative values belonging to ACP and OS. CONCLUSION: The percentage of the most complex and challenging type of ACP (the long, narrow, and narrow-angled ACP) in fetuses was found to be close to adults. Thus, routine adult surgical procedures such as anterior clinoidectomy might be successfully used in young children and infants. The attachment site of OS relative to ACP in adults was more anterior according to fetuses probably due to postnatal development such as the pneumatization of the sphenoid bone. In this regard, for pediatric neurosurgeons to avoid iatrogenic injuries and to select appropriate surgical approaches, further studies conducted on the attachment of OS relative to ACP in children are needed.

Estimation of sodium adsorption ratio in a river with kernel-based and decision-tree models.

The control of surface water quality plays an important role in the management of water resources. In this context, the estimation and assessment of sodium adsorption ratio (SAR) are required which is one of the significant water quality parameters in the agricultural production sector. Chemical analysis might not, however, be feasible for a longer period of time in all the country-scale rivers. Therefore in this study, a support vector regression (SVR) model with different kernel functions; K nearest neighbour algorithm; and four decision-tree models, namely, Hoeffding tree, random forest, random tree, and REPTree, were used to estimate the SAR value with minimal parameters in the Aladag River in Turkey. In alternative scenarios, a correlation matrix and sensitivity analysis were used to ascertain the model inputs from among the 15 distinct parameters. All 15 parameters were utilized as model inputs in the first scenario, and only the sodium (Na) parameter was utilized as the model input in the final scenario. The accuracy of the aforesaid models was then assessed making use of correlation coefficient, Nash-Sutcliffe model efficiency coefficient, root mean square error, mean absolute error, and Willmott index of agreement. The results indicate that the SVR model with the poly kernel function provides the best estimates of SAR among the considered models. According to the findings, there is no considerable difference between the results acquired in the first and last scenarios, and one can determine the SAR value while making use of machine learning approaches taking into account only Na parameter.

Autosomal dominant polycystic kidney disease: new role for ultrasound.

OBJECTIVES: To evaluate the accuracy of US in calculating renal volumes and renal resistive index (RRI) that was obtained using a new method in patients with autosomal dominant polycystic kidney disease (ADPKD). METHODS: In this prospective study, US and MRI were performed in 57 patients with ADPKD (31 female and 26 male; age range, 19-79 years) between August 2017 and May 2018. The volumes determined using US and MRI were compared. The ellipsoid formula was re-evaluated using different multipliers. RRI was obtained 1.5-2 cm distal to the outlet of main renal arteries. The relationship between mean RRI, renal function tests, and kidney volumes and difference between mean RRI of ADPKD patients with and without renal failure were investigated using a two-sided independent samples t test and Pearson correlation test. Interobserver agreements for volume assessments and RRI measurements were determined. RESULTS: By changing the ellipsoid formula, a very good agreement was found (ICC 0.970 for the right kidney and ICC 0.973 for the left kidney). The mean RRI in the right renal artery was 0.61 ± 0.07 and in the left renal artery 0.63 ± 0.06. The mean RRI of ADPKD patients with renal failure was significantly higher than that of patients without renal failure (p = 0.005). There was a significant correlation between mean RRI and renal function tests. CONCLUSION: The accuracy of the US in calculating renal volumes increases by adapting the ellipsoid formula. RRI may be used for the management of ADPKD independently of volumes. KEY POINTS: •The accuracy of ultrasonography for renal volume measurement increases by changing the classical ellipsoid formula. •Renal resistive index measured by color Doppler ultrasonography is helpful for the management of autosomal dominant polycystic kidney disease. •The role of Doppler US in autosomal dominant polycystic kidney disease should increase as a result of our findings.

Evaluation of the Foramen Magnum Area Calculated by Different Methods: A Radioanatomic Study.

PURPOSE: The main objective of the study was to evaluate the probable diversity in the area of the foramen magnum (FM) calculated by different measuring methods. METHODS: The study was conducted on 24 dry skulls, present in the collection of the Anatomy Department, Faculty of Medicine, Mersin University. The area of FM was calculated by different measurement methods including automatic field setting, Teixeria and Radinsky formulas obtained from anatomic (ASM), photographic (PSM) and radiologic (RSM) skull measurements. RESULTS: The areas of FMs calculated by Teixeria formula in RSM, PSM, and ASM were as follows: 857.96 ±â€Š99.97 mm, 796.68 ±â€Š105.08 mm, and 820.86 ±â€Š96.40 mm, respectively. The areas calculated by Radinsky formula in RSM, PSM, and ASM were as follows: 851.37 ±â€Š99.68 mm, 792.63 ±â€Š104.18 mm, and 814.85 ±â€Š94.99 mm, respectively. Lastly, the areas calculated by the automatic field setting of RSM and PSM software were as follows: 799.75 ±â€Š103.38 mm and 752.83 ±â€Š105.60 mm, respectively. CONCLUSION: Statistical significance was observed between the areas of FM obtained from RSM, ASM, and PSM when calculated by the automatic field setting, Teixeria formula, and Radinsky formula. The authors think that considering the amorphous shape of FM, the automatic field setting of the software should be used to obtain the most accurate numerical data related to the area of FM.

Renal stone composition does not affect the outcome of percutaneous nephrolithotomy in children.

PURPOSE: We sought to investigate the association between renal stone composition and percutaneous nephrolithotomy outcomes in pediatric patients and define the characterization of the stone composition. METHODS: The data of 1157 children who underwent percutaneous nephrolithotomy between 1991 and 2012 were retrieved from the multicenter database of the Turkish Pediatric Urology Society. The study population comprised 359 children (160 girls, 199 boys) with stone analyses. Patients were divided into five groups according to the stone composition [group 1: calcium oxalate; group 2: calcium phosphate; group 3: infection stones (magnesium ammonium phosphate, ammonium urate); group 4: cystine; group 5: uric acid, xanthine stones]. RESULTS: Patient characteristics, perioperative, postoperative, and stone characteristics were compared considering the stone composition. There were no significant differences between the groups concerning age, sex, side involved, preoperative hematocrit levels, and solitary renal unit. Patients with cystine stones were more likely to have a history of stone treatment. Groups 2 and 5 had mostly solitary stones. However, group 3 had staghorn stone more often, and group 4 frequently had multiple stones. Overall stone-free rate (79.4%) was similar among the groups. Although stone composition was related to blood transfusion and prolonged operative and fluoroscopy screening times on univariate analysis, it was not a significant predictor of them on multivariate analysis. CONCLUSIONS: Stone composition was not a predictor of outcomes of pediatric percutaneous nephrolithotomy. However, cystine and infection stones, which are larger and filled multiple calyxes due to the nature of stone forming, were more challenging cases that need multiple tracts.