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MotivationLarge Language Models (LLMs) are being adopted at an unprecedented rate, yet still face challenges in knowledge-intensive domains like biomedicine. Solutions such as pre-training and domain-specific fine-tuning add substantial computational overhead, requiring further domain-expertise. Here, we introduce a token-optimized and robust Knowledge Graph-based Retrieval Augmented Generation (KG-RAG) framework by leveraging a massive biomedical KG (SPOKE) with LLMs such as Llama-2-13b, GPT-3.5-Turbo and GPT-4, to generate meaningful biomedical text rooted in established knowledge.ResultsCompared to the existing RAG technique for Knowledge Graphs, the proposed method utilizes minimal graph schema for context extraction and uses embedding methods for context pruning. This optimization in context extraction results in more than 50% reduction in token consumption without compromising the accuracy, making a cost-effective and robust RAG implementation on proprietary LLMs. KG-RAG consistently enhanced the performance of LLMs across diverse biomedical prompts by generating responses rooted in established knowledge, accompanied by accurate provenance and statistical evidence (if available) to substantiate the claims. Further benchmarking on human curated datasets, such as biomedical true/false and multiple-choice questions (MCQ), showed a remarkable 71% boost in the performance of the Llama-2 model on the challenging MCQ dataset, demonstrating the framework's capacity to empower open-source models with fewer parameters for domain-specific questions. Furthermore, KG-RAG enhanced the performance of proprietary GPT models, such as GPT-3.5 and GPT-4. In summary, the proposed framework combines explicit and implicit knowledge of KG and LLM in a token optimized fashion, thus enhancing the adaptability of general-purpose LLMs to tackle domain-specific questions in a cost-effective fashion.Availability and implementationSPOKE KG can be accessed at https://spoke.rbvi.ucsf.edu/neighborhood.html. It can also be accessed using REST-API (https://spoke.rbvi.ucsf.edu/swagger/). KG-RAG code is made available at https://github.com/BaranziniLab/KG_RAG. Biomedical benchmark datasets used in this study are made available to the research community in the same GitHub repository.Supplementary informationSupplementary data are available at Bioinformatics online.

Chronic pancreatitis (CP) is a progressive benign fibroinflammatory condition involving repeated episodes of pancreatic inflammation, which lead to fibrotic tissue replacement and subsequent pancreatic insufficiency. A lifetime risk of developing pancreatic ductal adenocarcinoma (PDAC) in patients with chronic pancreatitis is reported to be 1.5%-4%. However, diagnosis of PDAC in patients with CP can be challenging, in part due to overlapping imaging features. In rare instances, pancreatic parenchymal calcifications that are typically associated with chronic pancreatitis may diminish in the case of a developing PDAC. In this article, we present a patient with chronic pancreatitis in whom calcifications decreased at the time of pancreatic ductal adenocarcinoma diagnosis, as compared to prior CT imaging. The unique imaging features of “diminishing calcifications” associated with a hypoattenuating lesion can potentially be a useful sign of pancreatic ductal adenocarcinoma and may aid in early diagnosis and prompt treatment intervention.

Abstract The medicinal plant Cannabis sativa L. (C. sativa) is currently being extensively studied to determine the full extent of its therapeutic pharmacological potential. Δ9-tetrahydocannabinol (THC) and cannabidiol (CBD) are the most thoroughly investigated compounds. We aimed to explore the anticancer activity of cannabinoids mixture isolated from the Lebanese C. sativa plant in ratios comparable to the local medicinal plant, to elucidate its mechanism of action in breast cancer cells in vitro. Cells were subjected to cytotoxicity assay, cell cycle analysis, Annexin V/PI dual staining, cell death ELISA, immunofluorescence, in addition to western blot analysis of apoptotic and autophagy markers. We further evaluated the anti-metastatic effect of cannabinoids on MDA-MB-231 using the scratch wound-healing, trans-well migration and invasion assays. Our results revealed the promising therapeutic benefits of CBD/THC on inhibiting the growth of breast cancer cells by promoting cellular fragmentation, phosphatidylserine translocation to the outer membrane leaflet and DNA fragmentation in both cell lines while inhibiting the motility of the triple negative breast cancer cells. In our study, CBD/THC mixture was found to exhibit a pro-apoptotic activity via the activation of the mitochondrial apoptotic pathway, independent from ROS production while also suggesting the activation of a caspase-dependent apoptotic pathway. Even though autophagy was altered upon exposure to the cannabinoid mixture, our data suggested that it is not the mechanism responsible of inducing cell death. In conclusion, our study demonstrates the promising therapeutic benefits of CBD and THC isolated from the Lebanese C. sativa plant on breast cancer cells in vitro.

Abstract Background Taste buds’ innervation is necessary to sustain their cell turnover, differentiated taste buds and nerve fibers in circumvallate papilla (CVP) disappear following glossopharyngeal nerve transection. Normally, taste buds recover to baseline number in about 70 days. Bone marrow stem cell (BM-MSC) derived exosomes or their combination with Zinc chloride are used to assess their potential to speed up the regeneration process of CVP following bilateral deafferentation. Methods Twenty-eight male Sprague-Dawley rats were randomly divided into four groups; Group I: subjected to sham operation followed by IP injection of saline. The other experimental groups (II, III and IV) were subjected to surgical bilateral transection of glossopharyngeal nerve. Group II received single IP injection of saline. Group III received single IV injection of BM-MSC-derived exosomes (100 µg). Group IV received single IV injection of BM-MSC-derived exosomes and single IP injection of zinc chloride (5 mg/kg). After 28 days, CVP was dissected and prepared for histological and histomorphometric analysis, RT-PCR for cytokeratin 8 gene expression, ELISA to assess protein level of brain-derived neurotrophic factor, redox state analysis of malondialdehyde and glutathione content, followed by statistical analysis. Results Histopathologically, group II exhibited great tissue damage with marked reduction in taste buds and signs of degeneration in the remaining ones. Group III was close to control group with marked improvement in taste buds’ number and structure. Group IV showed inferior results when compared to group III, with many immature taste buds and signs of degeneration. Statistical results showed that groups I and III have significantly higher values than groups II and IV regarding taste buds’ number, cytokeratin 8, and reduced glutathione. However, malondialdehyde demonstrated high significant values in group IV compared to groups I and III. Regarding brain-derived neurotrophic factor, group III had significantly higher values than group II. Conclusion BM-MSC-derived exosomes have superior regenerative potentials in acceleration of CVP and nerve healing following bilateral transection of glossopharyngeal nerve in contrary to its combination with zinc chloride. Graphical Abstract

Abstract Candida auris is an emerging nosocomial fungal pathogen associated with life-threatening invasive disease due to its persistent colonization, high level of transmissibility and multi-drug resistance. Aggregative and non-aggregative growth phenotypes for C. auris strains with different biofilm forming abilities, drug susceptibilities and virulence characteristics have been described. Using comprehensive transcriptional analysis we identified key cell surface adhesins that were highly upregulated in the aggregative phenotype during in vitro and in vivo grown biofilms using a mouse model of catheter infection. Phenotypic and functional evaluations of generated null mutants demonstrated crucial roles for the adhesins Als4112 and Scf1 in mediating cell-cell adherence, coaggregation and biofilm formation. While individual mutants were largely non-aggregative, in combination cells were able to co-adhere and aggregate, as directly demonstrated by measuring cell adhesion forces using single-cell atomic force spectroscopy. This co-adherence indicates their role as complementary adhesins, which despite their limited similarity, may function redundantly to promote cell-cell interaction and biofilm formation. Functional diversity of cell wall proteins may be a form of regulation that provides the aggregative phenotype of C. auris with flexibility and rapid adaptation to the environment, potentially impacting persistence and virulence.

Abstract The fall armyworm, Spodoptera frugiperda is the most distractive polyphagous noctuid pest in tropical and subtropical regions. The current study was designed to examine the insecticidal activity of the water extract of Moringa olifiera leaves cultivated from unirradiated and 40 Gy irradiated seeds. Also, the effect of the extract on some digestive enzymes activities was assayed. The results indicated that the extract produced from 40 Gy irradiated seeds was more effective than those of unirradiated one. As well as, leaves extract produced from cultivated irradiated and unirradiated seeds decrease lipase protease and amylase activities of 3rd instar larvae of S. frugiperda and the highest decrease was in larvae fed on leaves produced from irradiated cultivated seeds. Therefore, the water extract of M. olifiera leaves cultivated from 40 Gy irradiated seeds might be seen as an environmentally beneficial pest management method.

Abstract Background In liver computed tomography (CT), tailoring the contrast injection to the patient’s specific characteristics is relevant for optimal imaging and patient safety. We evaluated a novel algorithm engineered for personalized contrast injection to achieve reproducible liver enhancement centered on 50 HU. Methods From September 2020 to August 31, 2022, CT data from consecutive adult patients were prospectively collected at our multicenter premises. Inclusion criteria consisted of an abdominal CT referral for cancer staging or follow-up. For all examinations, a web interface incorporating data from the radiology information system (patient details and examination information) and radiographer-inputted data (patient fat-free mass, imaging center, kVp, contrast agent details, and imaging phase) were used. Calculated contrast volume and injection rate were manually entered into the CT console controlling the injector. Iopamidol 370 mgI/mL or Iohexol 350 mgI/mL were used, and kVp varied (80, 100, or 120) based on patient habitus. Results We enrolled 384 patients (mean age 61.2 years, range 21.1–94.5). The amount of administered iodine dose (gI) was not significantly different across contrast agents (p = 0.700), while a significant increase in iodine dose was observed with increasing kVp (p

Abstract The aim of this study is to evaluate the role of serum level of Interleukin 6(IL-6) and Interleukin 17 (IL-17) in liver transplantation outcome for living recipients, Analyze the relation between the gene polymorphism and the occurrence of rejection after liver transplantation and Study the relation between the gene polymorphism and the occurrence of different infectious complications. The study was conducted in March 2023 and included 60 healthy volunteers from the National Liver Institute (NLI) blood bank at Menoufia University and 120 live donation liver recipient patients at NLI. During one month of liver transplantation, the cytokine levels (IL-17, IL-6 proteins, IL-6 G-174C, and IL-17 A rs2275913 gene polymorphism) and CD4 levels for 60 patients of 120 live donation liver recipient patients whom early reject transplanted tissue and the same parameters were measured after 6 months follow up for non-reject group. The main finding of this study was that the post-transplant rejection group and the post-transplant non-rejection and control groups differed significantly in the genotype frequency (CC, CG, and GG) or alleles of IL-6 G-174C (p = 0.011). On the other hand IL-17A rs2275913 gene polymorphism and its alleles (p = 0.71) showed no statistically significant difference. We also observed that serum IL-17 levels, with 100% specificity and 100% sensitivity threshold, will be more sensitive and specific than serum IL-6 and CD4 count in differentiating post-transplant rejection from non-rejection patients. The results showed that there was no significant relationship between the genotypes and serum levels of interleukins and the type and degree of rejection. Proinflammatory cytokines might be useful indicators for distinguishing and early identifying unfavorable outcomes after transplantation, allowing for prompt and effective treatment intervention. To evaluate these findings, prospective clinical trials are required.

Abstract Wastewater treatment plants (WWTPs) contain a diverse array of microbes, underscoring the need for regular monitoring to ensure treatment efficacy and protect health. However, detailed studies on waste stabilization ponds (WSPs) are scarce. This study evaluates a full-scale WSP, located in Giza Governorate, Egypt, including anaerobic, facultative, and maturation ponds, examining an array of parameters such as enteric viruses, microeukaryotes (protozoa and algae), bacterial indicators, bacterial pathogens, and physicochemical characteristics. Utilizing multivariate statistical models, we identified significant distinctions in physicochemical parameters and microbial communities, primarily driven by treatment stages rather than temporal variations. In addition, seven viruses (human rotavirus, adenovirus, norovirus, astrovirus, hepatitis A virus, polyomavirus, and papillomavirus) were detected during the different stages (inlet, anaerobic, facultative, and outlet) of the WSP, except norovirus and papillomavirus were absent in the outlet stage. The viral log means reductions ranged from 1.24 to 5.94, depending on the stage and virus type. The removal efficiency of bacterial pathogens was more than 99%. High throughput 18S rRNA gene amplicon sequencing indicated the dominance of animal parasitic Apicomplexa species and Vermamoeba spp. in the WSP. Network analysis indicated significant roles for Ciliophora in virus reduction. Notably, the maturation pond's outlet was dominated by Spirulina maxima, whose mat-forming tendencies may inhibit pathogen removal by providing protective shelters. Although the WSP effectively reduced pathogen levels, the high initial loads resulted in considerable concentrations in the final effluent, posing ongoing public health concerns. This study highlights the imperative of including pathogen standards in national regulations for wastewater reuse.

Abstract Solvent extraction of selenium(IV) ions from highly concentrated hydrochloric acid using 0.4 mol/L Aliquat 336 dissolved in kerosene was investigated. As a modifying agent, 1-octanol (10% v/v) was added to the organic phase to avoid the third phase formation. The effect of different parameters affecting the liquid-liquid extraction of selenium(IV) such as the acid concentration, shaking time, metal ion concentration in the aqueous phase, loading capacity, diluents, and temperature, was studied. The results indicate that selenium(IV) is extracted efficiently by 0.4 mol/L Aliquat 336 dissolved in kerosene. It was noticed that the extraction increased with the increase in the acid and Aliquat 336 concentrations, reaching an extraction percentage of about 92% at 8 mol/L HCl and 97.1% at 1 mol/L extractant. The extracted organic species is postulated to be [H2SeO2Cl2.2R4NCl]org by using the slope analysis method, and the value of Kex for selenium(IV) extraction was found to be 26.17 ± 2 M− 2. The structure of the extracted organic species was confirmed by FT-IR. The effect of diluents using various aliphatic and aromatic diluents indicated that kerosene is the most preferred diluent. This is owing to safety ground purpose, economic consideration, the lower cost, availability, and lower toxicity. Thermodynamic parameters indicate the endothermic nature for the solvent extraction of selenium(IV) for the investigated system according to the positive value obtained of the enthalpy change (ΔH). Depending on the obtained results, the method was used to recover selenium(IV) from a simulated solution synthesized in hydrochloric acid medium, which is expected in anode slime leach liquor solution.

Endometriosis is a chronic disease characterized by the presence and growth of endometrial glands and stroma outside of the uterine cavity. The pathogenesis is unclear, but a common theory attributes the condition to retrograde menstruation into the peritoneal cavity via the fallopian tubes. Hormonal influence causes these ectopic tissues to undergo cyclical bleeding, resulting in subsequent inflammation and scar tissue formation; however, it can affect postmenopausal women. In rare instances, endometriotic lesions can obstruct the ureter and result in hydroureteronephrosis and subsequent loss of renal function. This condition presents with nonspecific symptoms and is known as an often-silent disease, resulting in challenging and delayed preoperative diagnosis. In this article, we report the case of an asymptomatic 65-year old female who was diagnosed with deep pelvic endometriosis, which obstructed the right distal ureter. We focus on optimizing diagnosis and management through the application of radiological imaging modalities, specifically computed tomography (CT) and magnetic resonance imaging (MRI).

We present a model for Professional Development (PD) for in-service generalist primary teachers of science. The Remote Classroom Modelling (RCM) model is specifically designed to address salient challenges in the context of professional isolation. We share the principles that supported the design of this PD prototype, and the insights and lessons learned from a pilot of the model. We employed open-ended questionnaires, individual interviews and focus group interviews using a qualitative exploratory study to capture the experiences of teachers and students involved in this trial. Our findings suggest that the model supports primary teachers in developing: (1) their technological, pedagogical, and content knowledge, (2) their leadership, and (3) their resourcefulness in science. Our analysis reveals two important factors underpinning the successful implementation of this model: participant engagement and expert support. We discuss the applicability of this model in different settings and propose an agenda to progress the development of the RCM.