High sulphur oil of Type II kerogen of the oil shales from Western Central Jordan based on molecular structure and kinetics.

Organic rich sedimentary rocks of the Late Cretaceous Muwaqqar Formation from the Lajjun outcrop in the Lajjun Sub-basin, Western Central Jordan were geochemically analyzed. This study integrates kerogen microscopy of the isolated kerogen from 10 oil shale samples with a new finding from unconventional geochemical methods [i.e., ultimate elemental (CHNS), fourier transform infrared spectroscopy and pyrolysis-gas chromatography (Py-GC)] to decipher the molecular structure of the analyzed isolated kerogen fraction and evaluate the kerogen composition and characteristics. The optical kerogen microscopy shows that the isolated kerogen from the studied oil shales is originated from marine assemblages [i.e., algae, bituminite and fluorescence amorphous organic matter] with minor amounts of plant origin organic matter (i.e., spores). This finding suggests that the studied kerogen is hydrogen-rich kerogen, and has the potential to generate high paraffinic oil with low wax content. The dominance of such hydrogen-rich kerogen (mainly Type II) was confirmed from the multi-geochemical ratios, including high hydrogen/carbon atomic of more than 1.30 and high A-factor of more than 0.60. This claim agrees with the molecular structure of the kerogen derived from Py-GC results, which suggest that the studied kerogen is mainly Type II-S kerogen exhibiting the possibility of producing high sulphur oils during earlier stages of diagenesis, according to bulk kinetic modeling. The kinetic models of the isolated kerogen fraction suggest that the kerogen conversion, in coincidence with a vitrinite reflectance range of 0.55-0.60%, commenced at considerably lower temperature value ranges between 100 and 106 °C, which have produced oils during the early stage of oil generation. The kinetic models also suggest that the commercial amounts of oil can generate by kerogen conversion of up to 50% during the peak stage of oil window (0.71-0.83%) at relatively low geological temperature values in the range of 122-138 °C. Therefore, further development of the Muwaqqar oil shale successions is highly approved in the shallowly buried stratigraphic succession in the Lajjun Sub-basin, Western Central Jordan.

Detecting HLA loss of heterozygosity within a standard diagnostic sequencing workflow for prognostic and therapeutic opportunities.

To enable interrogation of tumor HLA LOH as a clinical diagnostic for precision oncology, we developed and validated an assay that detects HLA LOH within the context of an FDA-approved clinical diagnostic test, Tempus xT CDx. Validation was conducted via: (1) analytical evaluation of 17 archival patient samples and 42 cell line admixtures and (2) independent clinical evaluation of LOH prevalence in the HLA-A gene (HLA-A LOH) across 10,982 patients. To evaluate the prognostic relevance of HLA-A LOH we assessed 256 immunotherapy-treated non-small cell lung cancer (NSCLC) patients. To determine the feasibility of prospectively identifying and enrolling HLA-A LOH patients into a clinical trial, we established BASECAMP-1 (NCT04981119). We observed a positive predictive agreement of 97% and a negative predictive agreement of 100% in samples with ≥ 40% tumor purity. We observed HLA-A LOH in 16.1% of patients (1771/10,982), comparable to previous reports. HLA-A LOH was associated with longer survival among NSCLC adenocarcinoma patients (HR = 0.60, 95% CI [0.37, 0.96], p = 0.032) with a trend towards shorter survival among squamous cell patients (HR = 1.64, 95% CI [0.80, 3.41], p = 0.183). In 20 months, we prospectively screened 1720 subjects using the Tempus AWARE program, identifying 26 HLA-A*02 LOH patients at 8 sites, with 14 (54%) enrolled into BASECAMP-1. In conclusion, we developed and validated an investigational assay that detects tumor HLA LOH within an FDA-approved clinical diagnostic test, enabling HLA LOH utilization in diagnostic, prognostic, and therapeutic applications.

The Assessment of Diabetic Ketoacidosis Awareness Among Diabetic Patients and Their Caregivers in Makkah, Saudi Arabia: A Cross-Sectional Study.

INTRODUCTION: Diabetic ketoacidosis (DKA) is a life-threatening complication of diabetes mellitus (DM). It occurs due to a decrease in the level of insulin and an increase in the level of glucose in the blood, which makes cells unable to use glucose as an energy source and begin to break fat into ketones; an overload of ketones levels in the blood can lead to DKA. The aim of the study is to assess awareness of DKA among diabetic patients and their caregivers in Makkah City, Saudi Arabia. METHODS: This study is a cross-sectional study collected through an online questionnaire of diabetic patients and their caregivers in Makkah City. A self-reported questionnaire designed in Arabic and English through the use of Google Forms, it distributed electronically via social media to the target population with the objectives of the survey. RESULTS: A total of 400 participants were included, 73% of them were males, while 27% were females. A 9% of the participants have been diagnosed with DKA. A high awareness level about DKA was found in 32.5% of participants, while 67.5% had a poor awareness level. Factors associated with a high level of awareness towards DKA are young age, being single, students and having a previous DKA diagnosis. CONCLUSION: Regarding our participants who have poor awareness of DKA, further education for diabetic patients and their caregivers about DKA is crucial to prevent life-threatening complications, and improve quality of life for these patients.

Caffeine and Purine Derivatives: A Comprehensive Review on the Chemistry, Biosynthetic Pathways, Synthesis-Related Reactions, Biomedical Prospectives and Clinical Applications.

Caffeine and purine derivatives represent interesting chemical moieties, which show various biological activities. Caffeine is an alkaloid that belongs to the family of methylxanthine alkaloids and it is present in food, beverages, and drugs. Coffee, tea, and some other beverages are a major source of caffeine in the human diet. Caffeine can be extracted from tea or coffee using hot water with dichloromethane or chloroform and the leftover is known as decaffeinated coffee or tea. Caffeine and its derivatives were synthesized via different procedures on small and large scales. It competitively antagonizes the adenosine receptors (ARs), which are G protein-coupled receptors largely distributed in the human body, including the heart, vessels, brain, and kidneys. Recently, many reports showed the effect of caffeine derivatives in the treatment of many diseases such as Alzheimer's, asthma, parkinsonism, and cancer. Also, it is used as an antioxidant, anti-inflammatory, analgesic, and hypocholesterolemic agent. The present review article discusses the synthesis, reactivity, and biological and pharmacological properties of caffeine and its derivatives. The biosynthesis and biotransformation of caffeine in coffee and tea leaves and the human body were summarized in the review.

Phylogenetic evidence of a possible Trichuris globulosa species complex in Arabian camels from Kuwait.

During a 1-year study, Trichuris adults were obtained after necropsy of Arabian camels (Camelus dromedarius) from a slaughterhouse in Kuwait. Morphological and molecular identification was performed to confirm the identity of the Trichuris specimens obtained from C. dromedarius. Fifteen male Trichuris specimens were selected, and molecular identification was performed using mitochondrial cytochrome c oxidase subunit I, 12S ribosomal RNA, 16S ribosomal RNA genes and the nuclear internal transcribed spacer 2 (ITS2) region. Through phylogenetic analysis, 2 distinct groups were obtained using the mitochondrial genes, where group 1 showed a close relationship to Trichuris globulosa while group 2 showed a close relationship to Trichuris ovis, providing molecular evidence of a possible T. globulosa species complex. Additionally, the nuclear ITS2 region did not provide enough resolution to distinguish between the 2 groups of Trichuris specimens. Observation of morphological characters revealed variations in the shape of the male spicule sheath, where specimens present either a globular posteriorly truncated swelling or the absence of posteriorly truncated swelling. Moreover, the variations in male spicule sheath does not corroborate with the results of molecular data, suggesting the limited use of this character for identification of T. globulosa. In conclusion, molecular analysis suggests a possible species complex in T. globulosa, with the mitochondrial genetic markers successfully differentiating between the 2 groups. The limited use of the male spicule sheath as a diagnostic character for identification of T. globulosa is suggested.

A Systematic Review and Meta-Analysis of Artificial Intelligence Tools in Medicine and Healthcare: Applications, Considerations, Limitations, Motivation and Challenges.

Artificial intelligence (AI) has emerged as a transformative force in various sectors, including medicine and healthcare. Large language models like ChatGPT showcase AI's potential by generating human-like text through prompts. ChatGPT's adaptability holds promise for reshaping medical practices, improving patient care, and enhancing interactions among healthcare professionals, patients, and data. In pandemic management, ChatGPT rapidly disseminates vital information. It serves as a virtual assistant in surgical consultations, aids dental practices, simplifies medical education, and aids in disease diagnosis. A total of 82 papers were categorised into eight major areas, which are G1: treatment and medicine, G2: buildings and equipment, G3: parts of the human body and areas of the disease, G4: patients, G5: citizens, G6: cellular imaging, radiology, pulse and medical images, G7: doctors and nurses, and G8: tools, devices and administration. Balancing AI's role with human judgment remains a challenge. A systematic literature review using the PRISMA approach explored AI's transformative potential in healthcare, highlighting ChatGPT's versatile applications, limitations, motivation, and challenges. In conclusion, ChatGPT's diverse medical applications demonstrate its potential for innovation, serving as a valuable resource for students, academics, and researchers in healthcare. Additionally, this study serves as a guide, assisting students, academics, and researchers in the field of medicine and healthcare alike.

Pyrimido[5,4-c]quinolines: Synthesis from 3,4-Di-functionallized Quinoline, Reactivity and Biological Activities.

Quinoline and pyrimidine moieties are ubiquitous components in both natural and synthetic compounds, showcasing diverse applications. The fusion of these well-known structures into hybrid molecules has garnered attention due to their intriguing biological properties. Particularly in the field of medicinal chemistry, numerous studies in the last decade have focused on pyrimido[5,4-c]quinoline ring systems (PyQs5,4-c). This review elucidates the synthesis of PyQs5,4-c and their derivatives using 3,4-difunctionalized quinoline as a key starting material. The preparation of PyQs5,4-c involves a series of chemical transformations, including the Friedländer, Ullmann and Biginelli reaction, Vilsmeier-Haack formylation, Suzuki coupling, and a one-pot three-component reaction. These synthetic routes not only offer access to diverse PyQs5,4-c derivatives.

Understanding risk factors for severe acute malnutrition among children during war conflict in yemen.

Severe acute malnutrition (SAM) is a major public health concern in Yemen, particularly in areas affected by ongoing conflict war. SAM is defined as a very low weight for height, by visible severe wasting, or by the presence of nutritional edema. The prevalence of SAM in Yemen has increased dramatically since the onset of the conflict. Prior studies have focused on evaluating prevalence, but this novel study aimed to assess the risk factors associated with SAM prevalence. Five thousand two hundred and seventeen patients of SAM admitted at 12 sentinel hospitals were enrolled, and data were collected and analyzed. Marasmus was the most common form. Numerous risk factors contribute to the high prevalence of SAM in Yemen, including food insecurity. The current conflict has hampered food production, distribution, and access. Awareness of risk factors can prevent SAM in the general population.

Functional screening of amplification outlier oncogenes in organoid models of early tumorigenesis.

Somatic copy number gains are pervasive across cancer types, yet their roles in oncogenesis are insufficiently evaluated. This inadequacy is partly due to copy gains spanning large chromosomal regions, obscuring causal loci. Here, we employed organoid modeling to evaluate candidate oncogenic loci identified via integrative computational analysis of extreme copy gains overlapping with extreme expression dysregulation in The Cancer Genome Atlas. Subsets of "outlier" candidates were contextually screened as tissue-specific cDNA lentiviral libraries within cognate esophagus, oral cavity, colon, stomach, pancreas, and lung organoids bearing initial oncogenic mutations. Iterative analysis nominated the kinase DYRK2 at 12q15 as an amplified head and neck squamous carcinoma oncogene in p53-/- oral mucosal organoids. Similarly, FGF3, amplified at 11q13 in 41% of esophageal squamous carcinomas, promoted p53-/- esophageal organoid growth reversible by small molecule and soluble receptor antagonism of FGFRs. Our studies establish organoid-based contextual screening of candidate genomic drivers, enabling functional evaluation during early tumorigenesis.

Integrating pharmacogenomic testing into paired germline and somatic genomic testing in patients with cancer.

Precision medicine has revolutionized clinical care for patients with cancer through the development of targeted therapy, identification of inherited cancer predisposition syndromes and the use of pharmacogenetics to optimize pharmacotherapy for anticancer drugs and supportive care medications. While germline (patient) and somatic (tumor) genomic testing have evolved separately, recent interest in paired germline/somatic testing has led to an increase in integrated genomic testing workflows. However, paired germline/somatic testing has generally lacked the incorporation of germline pharmacogenomics. Integrating pharmacogenomics into paired germline/somatic genomic testing would be an efficient method for increasing access to pharmacogenomic testing. In this perspective, the authors argue for the benefits of implementing a comprehensive approach integrating somatic and germline testing that is inclusive of pharmacogenomics in clinical practice.

Fate of Cryptosporidium and Giardia through conventional and compact drinking water treatment plants.

Over the past three decades, a notable rise in the occurrence of enteric protozoan pathogens, especially Giardia and Cryptosporidium spp., in drinking water sources has been observed. This rise could be attributed not only to an actual increase in water contamination but also to improvements in detection methods. These waterborne pathogens have played a pivotal role in disease outbreaks and the overall escalation of disease rates in both developed and developing nations worldwide. Consequently, the control of waterborne diseases has become a vital component of public health policies and a primary objective of drinking water treatment plants (DWTPs). Limited studies applied real-time PCR (qPCR) and/or immunofluorescence assay (IFA) for monitoring Giardia and Cryptosporidium spp., particularly in developing countries like Egypt. Water samples from two conventional drinking water treatment plants and two compact units (CUs) were analyzed using both IFA and qPCR methods to detect Giardia and Cryptosporidium. Using qPCR and IFA, the conventional DWTPs showed complete removal of Giardia and Cryptosporidium, whereas Mansheyat Alqanater and Niklah CUs achieved only partial removal. Specifically, Cryptosporidium gene copies removal rates were 33.33% and 60% for Mansheyat Alqanater and Niklah CUs, respectively. Niklah CU also removed 50% of Giardia gene copies, but no Giardia gene copies were removed by Mansheyat Alqanater CU. Using IFA, both Mansheyat Alqanater and Niklah CUs showed a similar removal rate of 50% for Giardia cysts. Additionally, Niklah CU achieved a 50% removal of Cryptosporidium oocysts, whereas Mansheyat Alqanater CU did not show any removal of Cryptosporidium oocysts. Conventional DWTPs were more effective than CUs in removing enteric protozoa. The contamination of drinking water by enteric pathogenic protozoa remains a significant issue globally, leading to increased disease rates. Infectious disease surveillance in drinking water is an important epidemiological tool to monitor the health of a population.

Evaluation of the Lingual Splitting Patterns and the Lateral Bone Cut Ends Following Mandibular Bilateral Sagittal Split Osteotomy Using Cone Beam Computed Tomography (CBCT).

The bilateral sagittal split osteotomy (BSSO) is the most popular orthognathic procedure performed by maxillofacial surgeons to treat skeletal class II and class III and to correct mandibular asymmetries. The study aimed to evaluate the lingual splitting patterns and lateral bone cut end (LBCE) in bilateral sagittal split osteotomy (BSSO) and their relation with the ramal thickness and the presence of impacted third molars using cone beam computed tomography (CBCT). This prospective observational study included patients with mandibular prognathism who were treated with BSSO with or without Le Fort I osteotomy. Cone beam computed tomography was used to measure the ramal thickness preoperatively and to evaluate the LBCE, and the lingual splitting patterns postoperatively. Twenty-one patients (42 sides) were included in this study. The most commonly observed lingual splitting pattern was type III (47.6%), while the most common LBCE was type B (59.5%). The bad split was encountered 8 times on 42 sides (16.7%). A nonsignificant relationship between the ramal thickness and bad splitting was observed ( P =0.901). Impacted third molars were present in 16 of the 42 sides (38.1%) and had no significant effect on the occurrence of bad splitting ( P =0.063). Type III lingual splitting pattern and type B LBCE were the most commonly observed patterns. No direct association was observed concerning the presence of impacted mandibular third molars and the thickness of the ramus with the occurrence of bad splitting.

Use of Nickel Oxide Catalysts (Bunsenites) for In-Situ Hydrothermal Upgrading Process of Heavy Oil.

In this study, Nickel oxide-based catalysts (NixOx) were synthesized and used for the in-situ upgrading process of heavy crude oil (viscosity 2157 mPa·s, and API gravity of 14.1° at 25 °C) in aquathermolysis conditions for viscosity reduction and heavy oil recovery. All characterizations of the obtained nanoparticles catalysts (NixOx) were performed through Scanning Electron Microscopy (SEM), Transmission Electron Microscopy (TEM), Atomic Force Microscopy (AFM), X-Ray and Diffraction (XRD), and ASAP 2400 analyzer from Micromeritics (USA), methods. Experiments of catalytic and non-catalytic upgrading processes were carried out in a discontinuous reactor at a temperature of 300 °C and 72 bars for 24 h and 2% of catalyst ratio to the total weight of heavy crude oil. XRD analysis revealed that the use of nanoparticles of NiO significantly participated in the upgrading processes (by desulfurization) where different activated form catalysts were observed, such as α-NiS, ß-NiS, Ni3S4, Ni9S8, and NiO. The results of viscosity analysis, elemental analysis, and 13C NMR analysis revealed that the viscosity of heavy crude oil decreased from 2157 to 800 mPa·s, heteroatoms removal from heavy oil ranged from S-4.28% to 3.32% and N-0.40% to 0.37%, and total content of fractions (ΣC8-C25) increased from 59.56% to a maximum of 72.21%, with catalyst-3 thank to isomerization of normal and cyclo-alkanes and dealkylation of lateral chains of aromatics structures, respectively. Moreover, the obtained nanoparticles showed good selectivity, promoting in-situ hydrogenation-dehydrogenation reactions, and hydrogen redistribution over carbons (H/C) is improved, ranging from 1.48 to a maximum of 1.77 in sample catalyst-3. On the other hand, the use of nanoparticle catalysts have also impacted the hydrogen production, where the H2/CO provided from the water gas shift reaction has increased. Nickel oxide catalysts have the potential for in-situ hydrothermal upgrading of heavy crude oil because of their great potential to catalyze the aquathermolysis reactions in the presence of steam.

Integration of tumor extrinsic and intrinsic features associates with immunotherapy response in non-small cell lung cancer.

The efficacy of immune checkpoint blockade (ICB) varies greatly among metastatic non-small cell lung cancer (NSCLC) patients. Loss of heterozygosity at the HLA-I locus (HLA-LOH) has been identified as an important immune escape mechanism. However, despite HLA-I disruptions in their tumor, many patients have durable ICB responses. Here we seek to identify HLA-I-independent features associated with ICB response in NSCLC. We use single-cell profiling to identify tumor-infiltrating, clonally expanded CD4+ T cells that express a canonical cytotoxic gene program and NSCLC cells with elevated HLA-II expression. We postulate cytotoxic CD4+ T cells mediate anti-tumor activity via HLA-II on tumor cells and augment HLA-I-dependent cytotoxic CD8+ T cell interactions to drive ICB response in NSCLC. We show that integrating tumor extrinsic cytotoxic gene expression with tumor mutational burden is associated with longer time to progression in a real-world cohort of 123 NSCLC patients treated with ICB regimens, including those with HLA-LOH.

Refining colorectal cancer classification and clinical stratification through a single-cell atlas.

BACKGROUND: Colorectal cancer (CRC) consensus molecular subtypes (CMS) have different immunological, stromal cell, and clinicopathological characteristics. Single-cell characterization of CMS subtype tumor microenvironments is required to elucidate mechanisms of tumor and stroma cell contributions to pathogenesis which may advance subtype-specific therapeutic development. We interrogate racially diverse human CRC samples and analyze multiple independent external cohorts for a total of 487,829 single cells enabling high-resolution depiction of the cellular diversity and heterogeneity within the tumor and microenvironmental cells. RESULTS: Tumor cells recapitulate individual CMS subgroups yet exhibit significant intratumoral CMS heterogeneity. Both CMS1 microsatellite instability (MSI-H) CRCs and microsatellite stable (MSS) CRC demonstrate similar pathway activations at the tumor epithelial level. However, CD8+ cytotoxic T cell phenotype infiltration in MSI-H CRCs may explain why these tumors respond to immune checkpoint inhibitors. Cellular transcriptomic profiles in CRC exist in a tumor immune stromal continuum in contrast to discrete subtypes proposed by studies utilizing bulk transcriptomics. We note a dichotomy in tumor microenvironments across CMS subgroups exists by which patients with high cancer-associated fibroblasts (CAFs) and C1Q+TAM content exhibit poor outcomes, providing a higher level of personalization and precision than would distinct subtypes. Additionally, we discover CAF subtypes known to be associated with immunotherapy resistance. CONCLUSIONS: Distinct CAFs and C1Q+ TAMs are sufficient to explain CMS predictive ability and a simpler signature based on these cellular phenotypes could stratify CRC patient prognosis with greater precision. Therapeutically targeting specific CAF subtypes and C1Q + TAMs may promote immunotherapy responses in CRC patients.

Protocol for drug screening of patient-derived tumor organoids using high-content fluorescent imaging.

High-content imaging of tumor organoids (TOs) treated with therapeutic agents provides detailed cell viability readouts at the organoid level. In contrast, most used protocols provide one number per well. While requiring the use of inverted microscopy with an automated stage, this protocol can provide critical information about heterogeneous responses of TOs to various treatments. This protocol describes a technique for culturing and drug testing TOs using fluorescent indicators of cell viability with high reproducibility. For complete details on the use and execution of this protocol, please refer to Larsen et al. (2021).

Privacy preserving validation for multiomic prediction models.

Reproducibility of results obtained using ribonucleic acid (RNA) data across labs remains a major hurdle in cancer research. Often, molecular predictors trained on one dataset cannot be applied to another due to differences in RNA library preparation and quantification, which inhibits the validation of predictors across labs. While current RNA correction algorithms reduce these differences, they require simultaneous access to patient-level data from all datasets, which necessitates the sharing of training data for predictors when sharing predictors. Here, we describe SpinAdapt, an unsupervised RNA correction algorithm that enables the transfer of molecular models without requiring access to patient-level data. It computes data corrections only via aggregate statistics of each dataset, thereby maintaining patient data privacy. Despite an inherent trade-off between privacy and performance, SpinAdapt outperforms current correction methods, like Seurat and ComBat, on publicly available cancer studies, including TCGA and ICGC. Furthermore, SpinAdapt can correct new samples, thereby enabling unbiased evaluation on validation cohorts. We expect this novel correction paradigm to enhance research reproducibility and to preserve patient privacy.

Case image and multimodal imaging of a fully-formed functional chorioretinal anastomosis using OCT angiography.

OCT-angiography description of a fully functional large-diameter chorioretinal anastomosis, or chorioretinal shunt in a 38-year-old female patient with a past history of congenital toxoplasmosis and resulting macular atrophy and scarring.

Targeted replacement of full-length CFTR in human airway stem cells by CRISPR-Cas9 for pan-mutation correction in the endogenous locus.

Cystic fibrosis (CF) is a monogenic disease caused by impaired production and/or function of the CF transmembrane conductance regulator (CFTR) protein. Although we have previously shown correction of the most common pathogenic mutation, there are many other pathogenic mutations throughout the CF gene. An autologous airway stem cell therapy in which the CFTR cDNA is precisely inserted into the CFTR locus may enable the development of a durable cure for almost all CF patients, irrespective of the causal mutation. Here, we use CRISPR-Cas9 and two adeno-associated viruses (AAVs) carrying the two halves of the CFTR cDNA to sequentially insert the full CFTR cDNA along with a truncated CD19 (tCD19) enrichment tag in upper airway basal stem cells (UABCs) and human bronchial epithelial cells (HBECs). The modified cells were enriched to obtain 60%-80% tCD19+ UABCs and HBECs from 11 different CF donors with a variety of mutations. Differentiated epithelial monolayers cultured at air-liquid interface showed restored CFTR function that was >70% of the CFTR function in non-CF controls. Thus, our study enables the development of a therapy for almost all CF patients, including patients who cannot be treated using recently approved modulator therapies.