Miracle-dz/UniFAR-FTUs huggingface dataset:
Radiotracer uptake classification using deep learning for evaluation of image-derived cancer biomarkers in PET/CT

In the care of patients with cancer, knowledge of the disease spread and overall burden is a key factor in the clinical decision-making process. Medical imaging is routinely used as noninvasive method to aid diagnosis and staging as well as treatment selection, planning, and monitoring. In addition to qualitative image inspection by physicians, standardized categorical and quantitative variables are increasingly used for accurate and reproducible image evaluation. Nevertheless, the manual determination of detailed image-derived parameters can require laborious examination and maneuvering, thus being time-consuming, error-prone, and operator dependent. Conversely, automated image analysis methods can be employed to improve robustness and repeatability. Notably, deep learning techniques have demonstrated high accuracy in automating visual tasks and are promising for enabling image-derived biomarkers in oncology. This dissertation presents contributions to image analysis methods in positron emission tomography (PET) / computed tomography (CT) and their application in determining image-derived biomarkers in oncology. The first contribution consists in a deep learning method for automated classification of elevated tracer uptake regions, trained for multiple radiotracers. PET/CT image regions are classified as uptake suspicious or nonsuspicious for cancer. Additionally, high-uptake regions are classified with respect to their anatomical location. Results indicate that a convolutional neural network can classify high uptake sites in good agreement with the visual assessment by a physician. The second contribution consists in the application of automated uptake classification in Prostate Specific Membrane Antigen (PSMA)-ligand PET/CT to assess prostate cancer stage. Results indicate that the proposed method can be used to determine the image-based nodal and metastatic stage according to a standardized reporting framework in concordance with expert reader evaluation. The third contribution consists in the application of automated uptake classification in 18F-Fluorodeoxyglucose (FDG) PET/CT images to estimate total metabolic tumor volume (TMTV) in lymphoma patients. Results show that in the examined cohort the proposed method determined an estimation of baseline TMTV significantly correlated and having comparable prognostic value with the TMTV estimation obtained semi-automatically by clinicians. The presented methods for automated analysis of PET/CT images using deep learning show promising results for supporting physicians in evaluating cancer stage and overall burden. Moreover, the investigated methods could potentially allow clinicians to identify novel biomarkers based on the rich information extracted from whole-body tumor assessment in PET/CT images. In conclusion, deep learning algorithms may aid the evaluation of informative and actionable image-derived cancer biomarkers and, together with diligent validation in multicenter trials, drive their establishment in the clinical routine.
Assessment of Muscluo-Tendionous Changes in Diabetes Mellitus: A Musculoskeletal Ultrasonographic study

Background: Diabetes mellitus (DM) is a common endocrine disorder worldwide, causing multisystem comorbidities, which compromise organ functions including musculoskeletal complications that affect the quality of life up to handicapping. Ultrasound is a very sensitive tool and a strong predictor of a DM musculoskeletal (MSK) changes, aiding in early management and control of disease parameters preventing subsequent comorbidities. Objective: This study aimed to evaluate if there is a relation between sonographic musculo-tendinous structural changes and diabetes and to correlate them with both clinical and laboratory parameters. Patient and Methods: 40 diabetic patients and 25 healthy subjects were involved in this work. All participants underwent history taking, general and musculoskeletal examination and laboratory and ultrasonographic evaluation. Results: 28 diabetic females and 12 diabetic males with mean age of 49.8± 13.7 years, showed statistically significant tendinous changes mainly tendon thickness compared to controls (p<0.05), there were statistically significant correlations between these variations and disease duration, HA1c P (0.008, <0.001) respectively. Conclusion: Chronic diabetes is linked to the destruction of collagen fibres, and biomechanical decline of tendons. Ultrasound is sensitive and accurate dedicated, simple and noninvasive screening method for the detection of musculoskeletal changes related to diabetes. This could serve as strong screening tool of underserved, asymptomatic diabetic individuals.
Semipolar InGaN-based superluminescent diodes for solid-state lighting and visible light communications

III-nitride light emitters, such as light-emitting diodes (LEDs) and laser diodes (LDs), have been demonstrated and studied for solid-state lighting (SSL) and visible-light communication (VLC) applications. However, for III-nitride LEDbased SSL-VLC system, its efficiency is limited by the “efficiency droop” effect and the high-speed performance is limited by a relatively small -3 dB modulation bandwidth (<100 MHz). InGaN-based LDs were recently studied as a droop-free, high-speed emitter; yet it is associated with speckle-noise and safety concerns. In this paper, we presented the semipolar InGaN-based violet-blue emitting superluminescent diodes (SLDs) as a high-brightness and high-speed light source, combining the advantages of LEDs and LDs. Utilizing the integrated passive absorber configuration, an InGaN/GaN quantum well (QW) based SLD was fabricated on semipolar GaN substrate. Using SLD to excite a YAG:Ce phosphor, white light can be generated, exhibiting a color rendering index of 68.9 and a color temperature of 4340 K. Besides, the opto-electrical properties of the SLD, the emission pattern of the phosphor-converted white light, and the high-speed (Gb/s) visible light communication link using SLD as the transmitter have been presented and discussed in this paper.
Multi-Omic Graph Diagnosis (MOGDx) : A data integration tool to perform classification tasks for heterogeneous diseases

Heterogeneity in human diseases presents challenges in diagnosis and treatments due to the broad range of manifestations and symptoms. With the rapid development of labelled multi-omic data, integrative machine learning methods have achieved breakthroughs in treatments by redefining these diseases at a more granular level. These approaches often have limitations in scalability, oversimplification, and handling of missing data. In this study, we introduce Multi-Omic Graph Diagnosis (MOGDx), a flexible command line tool for the integration of multi-omic data to perform classification tasks for heterogeneous diseases. MOGDx is a network integrative method that combines patient similarity networks with a reduced vector representation of genomic data. The reduced vector is derived from the latent embeddings of an auto-encoder and the combined network is fed into a graph convolutional network for classification. MOGDx was evaluated on three datasets from the cancer genome atlas for breast invasive carcinoma, kidney cancer, and low grade glioma. MOGDx demonstrated state-of-the-art performance and an ability to identify relevant multi-omic markers in each task. It did so while integrating more genomic measures with greater patient coverage compared to other network integrative methods. MOGDx is available to download from https://github.com/biomedicalinformaticsgroup/MOGDx. Overall, MOGDx is a promising tool for integrating multi-omic data, classifying heterogeneous diseases, and interpreting genomic markers.
Citations and Team Sizes

I explore whether small or large teams produce the most important astronomical results, on average, using citation counts as our metric. I present evidence that citation counts indicate the importance of papers. For the 1343 papers published in A&A, ApJ, and MNRAS in 2012 January-February, I considered 4.5 years worth of citations. In each journal, there are larger citation counts for papers from large teams than from small teams by a factor of about 2. To check whether the results from 2012 were unusual, I collected data from 2013 for A&A and found it to be the same as that for 2012. Could the preponderance of papers by large teams be due to self-citations (i.e., citing and cited papers sharing one or more authors)? To answer this, I looked at 136 papers with one to 266 authors and discovered a linear relation that ranges from a 12.7% self-citation rate for single-author papers to a 45.9% self-citation rate for papers with 100 authors. Correcting for these factors is not enough to explain the predominance of the papers with large teams. Then I computed citations per author. While large teams average more citations than small ones by a factor of 2, individuals on small teams average more citations than individuals on large teams by a factor of 6. The papers by large teams often have far more data, but those by small teams tend to discuss basic physical processes.
Evaluation of Outcomes and Complications of Large Volume Paracentesis without Albumin and Coagulopathy Therapy in Pediatrics with Severe Ascites

Background Large-volume paracentesis has become the first treatment choice for patients with severe and refractory ascites. The studies have reported several complications after therapeutic paracentesis. But there are few published data on the complications with or without Albumin therapy. We aimed to analyze the safety and complications of large-volume paracentesis in children with or without albumin therapy. Methods This study was conducted on children with severe ascites with chronic liver disease who underwent large-volume paracentesis. They were divided into albumin-infused and albumin non-infused groups. In the case of coagulopathy, no adjustment was made. Albumin was not administered after the procedure. The outcomes were monitored to evaluate the complications. To compare two groups, a t-test was utilized, and the ANOVA test was used to compare several groups. If the requirements for using these tests were not met, Mann-Whitney and Kruskal-Wallis tests were applied. Results Decreased heart rate was observed in all time intervals and was meaningful six days after paracentesis. MAP also decreased statistically at 48 hours and six days after the procedure (P < 0.05). Other variables did not show any meaningful change. Conclusion Children having tense ascites with thrombocytopenia, prolonged PT, Child-Pugh class C, and encephalopathy can undergo large-volume paracentesis without any complication. Albumin administration before the procedure in patients with low levels of Albumin (<2.9) can effectively overcome the problems of tachycardia and increased mean arterial pressure. There will be no need for Albumin administration after paracentesis.
Clinical and Therapeutic Profile of Non-Hodgkin’s Lymphoma: A Retrospective Study From a Najran Oncology Center

Background Non-Hodgkin lymphomas (NHL) represent a group of lymphoproliferative disorders, with a limited understanding of their clinical spectrum, primary extranodal variety, histopathology, and immunohistochemistry, particularly in developing countries. The objective of this study was to evaluate the clinicopathological characteristics and survival rates of NHL patients treated at King Khaled Hospital in Najran City, Saudi Arabia. Method In this retrospective chart review of NHL cases that received chemotherapy at the Oncology Center of King Khaled Hospital in Najran City, Saudi Arabia, between 2014 and 2021, we evaluated the clinicopathological features, survival rate, and associated factors. Using standardized data collection sheets, we extracted information on patients' age, gender, tumor type, stage, baseline laboratory evaluations, disease status, cancer treatment, and survival from electronic medical records. Univariate analysis was employed to identify factors associated with mortality and relapse. Results We included 43 NHL patients with a mean age of 59.23 ± 20.17 years, with a higher frequency among females (65.1%). B symptoms were present in 32 (74.4%) cases. The common primary site was peripheral lymph nodes (79.1%). Diffuse large B-cell lymphoma was the most common morphologic type (67.4%), and 46.5% of the patients had advanced-stage disease (stages III-IV). All patients received the first line of treatment, with the most common chemotherapy used being the RCHOP regimen (67.4%). Additionally, radiotherapy was performed in seven (16.3%) cases. Relapse occurred in eight (18.6%) cases with a median period of 47.5 months (Min: 20 - Max: 77 months). The mean overall survival time was 43.25 ± 2.98 months (range 12-168 months), and the one, three, and five-year survival rates were 91%, 58%, and 38%, respectively and the mortality rate was 32.6%. Univariate analysis showed that Burkitt lymphoma had (odds ratio (OR): 11.87; 95% confidence interval (CI): 1.58-89.09, p=0.016) and elevated lactate dehydrogenase (LDH) ((OR: 1.26; 95% CI: 0.35-4.54), p=0.014) were associated with mortality. Moreover, advanced age and the total number of first chemotherapy cycles were associated with relapse (p< 0.05). Conclusion The study highlights the variability of NHL cases, with a significant proportion presenting with advanced-stage disease and in middle age. The results suggest poor survival rates for patients with Burkitt lymphoma subtypes and elevated LDH levels.
Detection of quorum sensing virulence factor genes and its consanguinity to antibiotic sensitivity profile in the clinical isolates of Pseudomonas aeruginosa

Objective(s): Virulent strains of Pseudomonas aeruginosa exhibit multidrug resistance by intrinsic and extrinsic mechanisms which are regulated by quorum sensing signalling systems. This includes the production of auto-inducers and their transcriptional activators to activate various virulence factors resulting in host infections. The present study is thus aimed to detect the virulence factor production, quorum sensing activity, and susceptibility pattern of P. aeruginosa to antibiotics from clinical specimens. Materials and Methods: A total of 122 isolates of P. aeruginosa were phenotypically characterized by standard protocols and were categorized into MDR and non-MDR based on the antibiotic susceptibility profiles. Pyocyanin, alkaline protease and elastase production were assessed by qualitative and quantitative methods. Crystal violet assay was carried out for the quantification of biofilms. The genetic determinants of virulence were detected by PCR. Results: Out of the 122 isolates, 80.3% of isolates were MDR and the production of virulence factors was in positive correlation with the presence of genetic determinants and 19.6% were non-MDR, but still showed the production of virulence factors, as confirmed by both phenotypic and genotypic methods. Few carbapenem-resistant strains were detected which did not show the production of virulence factors by both methods. Conclusion: The study concludes, though the strains were non-MDR, they were still capable of producing the virulence factors which may be responsible for the dissemination and chronicity of the infection caused by P. aeruginosa.
Combined Phacoemulsification and STREAMLINE Surgical System Canal of Schlemm Transluminal Dilation in Eyes of Hispanic Patients with Mild to Moderate Glaucoma

Purpose To characterize clinical outcomes of transluminal dilation of the canal of Schlemm using the STREAMLINE Surgical System combined with phacoemulsification in eyes of Hispanic patients diagnosed with mild to moderate primary open-angle glaucoma. Methods This was a prospective analysis of all cases performed and followed up to 12 months. All eyes underwent medication washout preoperatively. Reduction in intraocular pressure (IOP) from unmedicated baseline, as well as medications from pre-washout baseline, were analyzed at postoperative Day 1, Week 1, and Months 1, 3, 6, 9, and 12. Results All 37 patients were Hispanic, 83.8% were female, and mean (standard deviation) age was 66.0 (10.5) years. Mean medicated preoperative IOP was 16.9 (3.2) mmHg using a mean of 2.1 (0.9) medications, unmedicated baseline IOP (after washout) was 23.2 (2.3) mmHg, and mean IOP at every postoperative study visit was significantly lower (p<0.0002). Mean IOP from month 1 through the first postoperative year ranged from 14.7–16.2 mmHg, representing a reduction of 7.0–8.5 mmHg (30.7–36.5%). At month 12, 80% of all eyes (28/35) and 77.8% of medication-free eyes (14/18) had IOP reduction ≥20% from unmedicated baseline, and 51.4% of eyes (18/35) were medication-free. Mean medication use was significantly reduced (by 59.9–74.6%, p<0.0001) at every postoperative study visit. The only adverse event occurring in >1 eye was high IOP (n=4) which was responsive to topical medical therapy; no adverse events were attributed to the transluminal dilation procedure. Conclusion Transluminal dilation of the canal of Schlemm using the STREAMLINE Surgical System combined with phacoemulsification safely and effectively reduced both IOP and dependence on IOP-lowering medications in a Hispanic population diagnosed with POAG and should be considered at the time of phacoemulsification in Hispanic patients who have a need for IOP reduction, medication reduction, or both.
Galcanezumab-Induced Myasthenia Gravis-Like Symptoms

Fluctuating weakness affecting the ocular, bulbar, and/or appendicular muscles is characteristic of myasthenia gravis. Autoimmune components and certain drugs have been implicated in the pathophysiology of this disease. I report a case of chronic migraine in which the patient developed symptoms of myasthenia gravis after using galcanezumab, the recently approved anti-calcitonin gene-related peptide (anti-CGRP). This case shows that anti-CGRP medications could affect the neuromuscular junction and cause such symptoms. Moreover, this case illustrates the clinical approach and management of such a presentation.
It is Possible to Reduce Ureteral Stent Clogging and Stent-Related Symptoms to Soothe the Pain of the Patient: A Case Report

Introduction Ureteral stent obstruction hinders the management of malignant diseases. Adequate stent insertion through an obstructed ureter does not necessarily guarantee renal decompression and stent-related symptoms adversely affect patient comfort. There are two major problems associated with ureteral stents: obstruction and intolerance to the stents. Case Presentation A 45-year-old woman was treated for cervical cancer with metastatic lymph nodes and ureteral obstruction with chemotherapy, radiotherapy, immunotherapy, and bilateral retrograde stenting. After recurrent stent obstruction, stent replacement was attempted more than 18 times over two years. In addition, stent-related symptoms adversely affected patient comfort. The patient was finally fitted with Superglide 8-French reinforced ureteral stents. Their replacement every six months was viewed by the patient as a relief compared to the all too frequent replacement of the previous stents. Moreover, the customized changes in the shape of Superglide stents improved patient comfort. Discussion Recent publications tend to indicate that large-lumen ureteral stents are most likely to remain permeable over time. Various modifications of the bladder or endo-ureteral part of double-pigtail stents have been increasingly reported, with the aim of improving their tolerance while maintaining effective drainage. Conclusion Adaptation of the internal lumen and shape of stents to the characteristics of the tumor and patient measurements appears to be important for increasing the drainage and tolerance of ureteral stents. The top priority for future ureteral stents suitable for malignant diseases should be to integrate these characteristics based on state-of-the-art data.
Ovarian Volume of Saudi Children and Adolescents in the Southern Region Based on Ultrasound Imaging

Introduction Sonography is a non-invasive and painless technique used for assessing pelvic anatomy and disorder in children and adolescents. Ovarian growth patterns during infancy and puberty are not completely understood. No consensus exists about the normal measures and morphologic appearance of the ovaries in the southern region of Saudi Arabia. Therefore, this study determined the pattern of ovarian and uterine sizes among Saudi girls and their correlation with age. Methods This study was conducted in the radiology department at Abha Maternity and Children Hospital among girls between 0-13 years. All the participants underwent transabdominal ultrasound, and we measured ovarian volume, uterine length, and endometrial thickness to correlate with chronologic age using the Chi-squared test. Results A Total of 152 females were included in this study. The median age was 72 months, with a minimum of one month and a maximum of 156 months. The Chi-squared test showed a significant correlation between age and ovarian measurement. Age was positively associated with ovarian volume, uterine length, and endometrial thickness (p<0.001). Conclusion The study concluded that age strongly correlated with the size of the uterus and ovaries, which is crucial in interpreting ultrasound measurements of the pelvic organs correctly.
The Impact of Socioeconomic Inequality on Mental Health among Adolescents in Qazvin, Iran: Blinder-Oaxaca Decomposition Method

Background Mental health is integral to public health in adolescents. Although previous studies have shown that low socioeconomic status (SES) is associated with mental disorders (MD), it is unclear which mental health domains are most important. Thus, our study aimed to investigate the associations between 5 domains of mental disorder and SES inequality in adolescents. Methods We conducted a cross-sectional study among adolescents (N = 1724). Associations between SES inequality with mental disorders, such as emotional symptoms, conduct problems, hyperactivity, peer relationship problems, and prosocial behavior, were examined. We used the concentration index (CI) to determine inequality. The gap between the low and high socioeconomic groups was decomposed into its determinants using the Blinder-Oaxaca decomposition method. Results Mental health's overall CI was –0.085 (P ˂ 0.001). The emotional problem was primarily caused by SES inequality (–0.094 [P = 0.004]). Decomposition of the gap between the 2 economic groups showed that physical activity, school performance, exercise, parents' smoking status, and gender were the most important determinants of inequality. Conclusion SES inequality plays a vital role in adolescents' mental health. It seems that the emotional problem domain of mental health might be more amenable to interventions than other domains.