Glass Slides Research Articles

Abstract 7486: Development and analytic validation of an ARv7/PSMA dual biomarker circulating tumor cell assay

Abstract Background Prostate cancer drug targets and biomarkers may be investigated non-invasively on circulating tumor cells (CTCs) obtained via liquid biopsies. PSMA is an important drug target in prostate cancer, and ARv7 is a splice variant that confers resistance to second-generation androgen receptor inhibitors. In this study, we describe the development and analytic validation of a novel assay to quantify ARv7 and PSMA protein expression on CTCs. The assay was validated with blood samples from patients with Stage IV prostate cancer to demonstrate clinical feasibility. To our knowledge, a PSMA/ARv7 dual protein assay for CTCs has not previously been reported. Methods LNCaP (PSMA positive), PC3 (PSMA negative), 22Rv1 (ARv7 positive), and BT474 (ARv7 negative) cells were spiked into healthy donor blood to generate model CTCs. Nucleated cells were collected from these spike-in samples using the AccuCyte® sample preparation kit and spread onto microscope slides. Slides were fixed and stained with antibodies to cytokeratin, EpCAM, and CD45 to detect CTCs and exclude white blood cells (WBCs), and with PSMA and ARv7 to evaluate protein expression on identified CTCs. The slides were imaged with the CyteFinder® automated immunofluorescence scanning microscope that identifies CTCs for confirmation by trained reviewers based on machine learning algorithms and quantitatively measures biomarker signal mean fluorescence intensity (MFI). Results For ARv7/PSMA expression classification of the model CTCs, the dual biomarker assay showed analytic sensitivity of 83%/97% and specificity 98%/99%, yielding accuracy of 90.2%/97.9%, respectively. The dynamic range of MFI for both biomarkers was approximately three orders of magnitude. Inter-run reproducibility CV was 13.6% (ARv7) and 6.9% (PSMA). Slide repeatability mean CV was 11.1% (ARv7) and 12.0% (PSMA). Clinical feasibility of the assay was investigated in 9 progressing Stage IV prostate cancer patient blood samples. CTCs were identified in all clinical samples (median 4, range 1 - 384). Thresholds for biomarker positivity were established based on MFI measurements of positive and negative control cell lines. ARv7 positivity in clinical samples ranged from 33% to 100%, and PSMA positivity ranged from 0% to 75%. Conclusions We have developed a dual ARv7/PSMA assay that simultaneously measures protein expression of both biomarkers on individual CTCs. The assay is accurate and reproducible for the assessment of ARv7 and PSMA expression by liquid biopsy in clinical studies. Citation Format: Jon Ladd, Erin Bayer, Brock Bartels, Eric Kaldjian, Arturo Ramirez. Development and analytic validation of an ARv7/PSMA dual biomarker circulating tumor cell assay [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7486.

Abstract 3511: iQC: machine-learning-driven prediction of surgery reveals systematic confounds in cancer whole slide images from hospitals by protocol

Abstract Problem: This 21st century has produced an eruption of research using AI for the detection and diagnosis of cancer. Yet, an often-unspoken core premise in this field of computational pathology is that a glass slide suitably represents the patient’s disease. Here, we report systematic confounds may dominate slides from a medical center, such that slides are unsuitable for diagnosis. Methods: We mathematically define high quality data as a whole slide image set where the patient’s surgery may be accurately predicted by an automated system. Our system “iQC” accurately distinguished biopsies (i.e. thin strands of tissue) from nonbiopsies, e.g. transurethral resections (TURPs) or prostatectomies, only when the data appeared high quality, e.g. bright histopathology stains and few artifacts. Thus, when the data are of high quality, iQC (i) accurately classifies pixels as tissue, (ii) accurately generates stats that describe the distribution of tissue, and (iii) accurately predicts surgical procedure from those stats. We compare iQC against the published HistoQC tool. Results: iQC holds all data to the same objective quality standard. We validate this standard in five Veterans Affairs Medical Centers (VAMCs) and the public Automated Gleason Grading Challenge (AGGC) dataset. For the surgery prediction task, we report an AUROC of 0.9966-1.000 at VAMCs that produced high quality data and AUROC=0.9824 for AGGC. In contrast, we report AUROC=0.7115 at the VAMC that produced poor quality data. A pathologist found poor quality may be explained by faded histopathology stains and VAMC protocol differences. Supporting this, iQC's novel stain strength statistic finds this VAMC had weaker stains (p < 2.2e-16, two-tailed Wilcoxon rank-sum test; Cohen's d=1.208) than the VAMC that contributed most of the slides. Additionally, iQC recommended only 2 of 3736 (0.005%) VAMC slides for review due to inadequate tissue. In contrast, HistoQC in its default configuration excluded 89.9% of VAMC slides because tissue was not detected, but we reduced this to 16.7% with our custom HistoQC configuration. Conclusion: Our surgery prediction AUROC may be a quantitative indicator positively associated with data quality for a dataset. Unless data are poor quality, iQC accurately locates tissue in slides and excludes few slides. iQC is, to our knowledge, the first automated system in computational pathology that validates quality against objective evidence, e.g. surgical procedure data available in the EHR/LIMS, which requires no efforts or annotations from anatomic pathologists. Citation Format: Andrew J. Schaumberg, Michael S. Lewis, Ramin Nazarian, Ananta Wadhwa, Nathanael Kane, Graham Turner, Purushotham Karnam, Poornima Devineni, Nicholas Wolfe, Randall Kintner, Matthew B. Rettig, Beatrice S. Knudsen, Isla P. Garraway, Saiju Pyarajan. iQC: machine-learning-driven prediction of surgery reveals systematic confounds in cancer whole slide images from hospitals by protocol [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3511.

Abstract 1161: Deep spatial proteomics: A new approach for obtaining insight into the glioblastoma microenvironment

Abstract Glioblastoma is the most frequent and malignant brain tumor, with a median survival of approximately 14 months. The tumor microenvironment is composed of different cell types and is known to support the glioblastoma cells and contribute to poor patient prognosis. Since accumulating studies report discordance between mRNA and protein abundances both on population and single-cell levels, and since proteins are the effector molecules of the cells and the actual target molecules of most drugs, our aim is to dissect the tumor microenvironment by spatial LC-MS based proteomics. Glioblastoma formalin-fixed paraffin-embedded (FFPE) tissue was sectioned and placed on membrane glass slides suitable for laser capture microdissection (LCM), followed by precise isolation of single cells from the heterogeneous tumor microenvironment. We used the Zeiss Palm MicroBeam laser microdissection instrument, combined with an Orbitrap Eclipse Tribrid Mass Spectrometer running our in-house sensitivity tailored Data Independent Acquisition method (WISH-DIA) to analyze and quantify the proteomes. We obtained up to 3000 proteins out of only 100 cells and were able to demonstrate the feasibility of collecting and analyzing various cell types at the single-cell level. The proteins identified belonged to many different classes/families of proteins and were able to distinguish the different cell types. In conclusion, this on-going study demonstrates our ability to isolate single cells from the highly heterogeneous tumor microenvironment of glioblastoma with ultra-high sensitivity, thereby allowing the characterization of the proteome of the glioblastoma microenvironment followed by identification of potential therapeutic and/or diagnostic targets. Citation Format: Kartikey Saxena, Rune Daucke, Vilde Pedersen, Pia Helene Klausen, Erwin Schoof, Bjarne Winther Kristensen. Deep spatial proteomics: A new approach for obtaining insight into the glioblastoma microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1161.

Abstract 3645: Unraveling spatial complexity of the tumor microenvironment: A whole transcriptomic perspective with Visium HD

Abstract In recent years, advances in spatial transcriptomics have revolutionized our understanding of the tumor microenvironment, providing crucial insights into the complex interplay of different cell types within cancer tissues. In this study, we employed the new, high definition Visium spatial transcriptomics assay (Visium HD) to investigate the intricate molecular landscape of prostate cancer at single-cell scale resolution and across the whole transcriptome. Our research focused on deciphering the spatial heterogeneity of gene expression patterns within the tumor microenvironment, shedding light on the interactions between cancer cells, stromal cells, and vasculature. The Visium HD assay enables an unbiased exploration of the transcriptome on FFPE tissue sections mounted on standard glass slides. Combining gene expression data with H&E images from the same section, it allows precise characterization of local molecular features and disease states at single-cell scale. We analyzed a set of human prostate adenocarcinoma samples with the Visium HD assay, and identified spatially regulated gene signatures associated with specific cell types and functional pathways. Our findings have recapitulated previously identified molecular markers, including VEGFA and MYC which have been implicated in tumor progression and angiogenesis. The spatial gene expression patterns had good correlation with histological annotations of cancerous and normal tissue within the H&E image. However, Visium HD allowed us to further observe molecular processes and pathways specific to this adenocarcinoma sample. This integrative approach offers valuable implications for personalized cancer therapy and the development of targeted interventions tailored to the spatial context of individual tumors. Our study underscores the significance of understanding the spatial organization of the whole transcriptome in cancer tissues, and highlights the potential of the Visium HD platform as a powerful tool for unraveling the complexities of the tumor microenvironment. These insights pave the way for the development of innovative therapeutic strategies and precision medicine approaches, ultimately contributing to improved outcomes for cancer patients. Citation Format: Yifeng Yin, Jerald Sapida, David Sukovich, David Patterson, Augusto Tentori. Unraveling spatial complexity of the tumor microenvironment: A whole transcriptomic perspective with Visium HD [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3645.

Abstract 3521: Robust inference of PTEN deletion in prostate cancer from routine histopathology whole slide images using attention-based deep learning

Abstract The diagnostic workup of prostate cancer (PCa) requires a thorough manual histopathological inspection of prostate tissue specimens stained with hematoxylin and eosin (H&E). While immunohistochemistry and advanced molecular tests like FISH could uncover key genetic alterations, they are not cost-effective and often require special training, necessitating the development of more effective tools that can accurately infer the status of such alterations directly from the tissue morphology depicted in routine H&E-stained glass slides. PTEN deletion, which is present in 15-20% of PCa, is significantly associated with tumor aggressiveness and negative prognostic impact. Deep learning (DL) models can be trained to predict the presence of PTEN deletion on routine whole slide images (WSIs) and select patients that could benefit from further treatment. In this study, we trained and tested the performance of a weakly supervised, multiple-instance learning network on a cohort of 449 WSIs radical prostatectomy specimens stained with hematoxylin & eosin. Our model demonstrated robust performance in predicting PTEN loss based on tumor morphology alone. Through the model, we also generated attention heatmaps of the most informative tiles of each slide, allowing us to quantify the different cellular components, thus inferring the morphological features associated with PTEN loss. This study shows that DL is a potential tool that can assist the pathologist in accurately inferring the molecular status of key genetic alterations using the tissue morphology depicted in histopathology slides. Moreover, the morphological information that can be obtained by attention-based models can be leveraged to close the gap between the pathologist’s morphological analysis and the interpretability of artificial intelligence models. Citation Format: Federico Scarfò, Mohamed Omar, Luigi Marchionni. Robust inference of PTEN deletion in prostate cancer from routine histopathology whole slide images using attention-based deep learning [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3521.

Abstract 6562: Comprehensive liquid biopsy: Multi-analyte evaluation of cellular and plasma components of blood in prostate cancer from a single blood collection tube

Abstract Background Liquid biopsy samples offer a non-invasive method for investigating drug targets and biomarkers in solid tumors. In this study, we describe a comprehensive liquid biopsy analysis of whole blood to identify circulating tumor cells (CTCs), large extracellular vesicles and CTC fragments, and CTC-white blood cell hybrids; quantify protein biomarker expression on CTCs; perform targeted mutation profiling on CTCs and cell-free DNA (cfDNA) from plasma; and analyze protein expression on white blood cells (WBCs) from a single 7.5 mL blood sample. This array of tests was applied to blood samples from patients with Stage IV prostate cancer to demonstrate clinical feasibility. Methods A novel dual biomarker CTC assay was developed to measure protein expression of PSMA and ARv7 on CTCs from stage IV prostate cancer patients. Nucleated cells from clinical samples were processed to microscope slides using AccuCyte®, an unbiased, density-based separation method that also allows for plasma collection for downstream analysis. Slides were fixed and stained with antibodies to cytokeratin, EpCAM, and CD45 to detect CTCs and exclude WBCs, and with PSMA and ARv7 to evaluate protein biomarker expression on identified CTCs. The slides were imaged with the CyteFinder® automated immunofluorescence scanning microscope that identifies CTCs for confirmation by trained reviewers and quantitatively measures protein mean fluorescence intensity (MFI) on any cells detected on the slides (CTCs, CTC-WBC hybrids, large extracellular vesicles and CTC fragments and WBCs). Individual CTCs and control pools of WBCs from clinical samples with at least 4 CTCs were picked using CytePicker®, a needle-based system used to isolate single cells. cfDNA was isolated from plasma removed during the AccuCyte® process using a QIAamp MinElute ccfDNA kit. Picked CTCs, WBC pools, and isolated ctDNA were sequenced using the OncoZoom Cancer HotSpot panel from Paragon Genomics. Results Nine progressing Stage IV prostate cancer patient blood samples were stained with a novel PSMA/ARv7 dual biomarker assay. CTCs were identified in all clinical samples (median 4, range 1 - 384). PSMA positivity in clinical samples ranged from 0% to 75%, and ARv7 positivity ranged from 33% to 100%, and. Additional analysis using QuPath was performed to determine PSMA/ARv7 protein expression on WBCs and CTC fragments. ctDNA analysis from 5 individual samples was compared to sequencing results from individual CTCs from the same samples. Conclusions Using a single 7.5 mL blood liquid biopsy, we can measure protein expression on enumerated CTCs and quantify these same protein biomarkers on WBCs and CTC fragments/oncosomes, determine the genetic makeup of the tumor through the sequencing of cfDNA, and monitor genetic mutations in intact CTCs in circulation. Citation Format: Jon Ladd, Erin Bayer, Brock Bartels, Arista Tischner, Rachel Ponting, Eric Kaldjian, Arturo Ramirez. Comprehensive liquid biopsy: Multi-analyte evaluation of cellular and plasma components of blood in prostate cancer from a single blood collection tube [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 6562.

Self-assembling photonic crystal film composed of TiO2/SiO2 hollow spheres for ultra-sensitive and reusable all-dielectric SERS substrates

Surface-enhanced Raman scattering (SERS) substrates were fabricated using an accurately designed arrangement of porous TiO2/SiO2 hollow spheres, notably devoid of noble metals. The synthesis of the SERS substrate involved the production of monodispersed composite materials through a hard-template technique. Subsequently, these hollow spheres were organized into an ordered photonic crystal (PC) film on glass slides using a dip-coating method. The porous SiO2 inter shell possessed a robust structure that significantly bolstered the durability of the SERS substrate. Moreover, the high specific surface area increased analyte absorbance, enhancing interaction with incident light. Simultaneously, the TiO2 outer shell facilitated charge transfer and heightened the reflective intensity of the substrate. The ordered arrangement of the TiO2/SiO2 hollow spheres, characterized by a substantial refractive-index contrast, resulted in a PC capable of augmenting the overall light reflectivity of the SERS substrate, thereby physically amplifying Raman signal intensity. Exploiting these distinctive properties, the TiO2/SiO2 substrate demonstrated an impressive detection limit of less than 10−10 M for both Methylene Blue and Rhodamine 6 G. Additionally, the enhancement factor (EF) reached a remarkable 4.7 × 107. The TiO2/SiO2 film's reusability and the straightforward preparation procedure position it as a promising candidate for future SERS analysis applications.

Effect of Malaria and Schistosoma mansoni Coinfection on Selected Biochemical Profiles among Patients Attending Selected Health Institutions at Dembiya, Northwest Ethiopia.

Malaria and schistosomiasis are infectious diseases that cause biochemical abnormalities. Malaria and Schistosoma mansoni coinfection causes exacerbations of health consequences and comorbidities. The study area is found in Ethiopia, where coinfection of malaria and S. mansoni is common. However, there is limited data on the biochemical profiles of patients coinfected with malaria and S. mansoni schistosomiasis in the study area. Hence, this study aimed to assess the effect of malaria and S. mansoni schistosomiasis coinfection on selected biochemical profiles. An institutional-based comparative cross-sectional study was conducted from March 30 to August 10, 2022. Using a convenient sampling technique, 70 participants (35 cases and 35 controls) were enrolled in the study. Schistosoma mansoni was detected in stool samples using the wet mount and the Kato Katz method. To detect Plasmodium, both thick and thin blood films were prepared and stained with Giemsa. The blood sample was processed for the analysis of biochemical profiles. All data were analyzed using SPSS version 25. A p value of less than 0.05 was considered statistically significant. The mean values of alanine aminotransferase and aspartate aminotransferase (37.1 U/L and 41.9 U/L, respectively) in coinfected participants were significantly higher than in the healthy control participants (17.4 U/L and 22.0 U/L, respectively) (p < 0.05). Also, the median values of creatinine, total bilirubin, and direct bilirubin (1.51 mg/dL, 2.35 mg/dL, and 0.91 mg/dL, respectively) in coinfected participants were significantly higher than in the healthy control participants (0.85 mg/dL, 0.42 mg/dL, and 0.12 mg/dL, respectively) (p < 0.05). However, median values of total protein (4.82 g/dL) and mean values of glucose (66.6 mg/dL) in coinfected participants were significantly lower than in the healthy control participants (total protein (7.64 g/dL) and glucose (91.9 mg/dL)) (p < 0.05). The results of biochemical profiles in healthy participants were significantly different from those with light, moderate, and heavy S. mansoni infection intensity in malaria and S. mansoni coinfection (p < 0.05). Schistosoma mansoni infection intensity had a positive correlation with biochemical profiles except for total protein and glucose, which correlated negatively in coinfected participants (p > 0.05). Biochemical profiles in coinfection were significantly changed as compared to healthy individuals. As a result, biochemical profile tests should be utilized to monitor and manage coinfection-related problems, as well as to reduce coinfection-related morbidity and death.

Six-orders-of-magnitude-spanning dispersion measurement via Kalman filtering-aided white-light interferometry.

Dispersion plays a great role in ultrafast laser oscillators, ultrashort pulse amplifiers, and many other nonlinear optical dynamics. Therefore, dispersion measurement is crucial for device characterization, system design and nonlinear dynamics investigation therein. In this work, we demonstrate a versatile approach, i.e., Kalman filtering-aided white-light interferometry, for group delay dispersion (GDD) characterization. Extended Kalman filter is adopted to track the cosine-like interferogram, and to eliminate the unintended bias and the envelope, providing a nearly ideal phase retrieval and GDD estimation. The measurement range could span from tens of fs2 to tens of ps2, with an uncertainty of about 0.1%, enabling precise GDD measurement for diverse optical components, ranging from a millimeter-thick glass slide to highly dispersive chirped fiber Bragg gratings. Benefited by the simplicity, convenient setup, and easy operation as well as relatively low cost, this approach would help photonic device characterization, dispersion management and nonlinear dynamics investigation in the laboratory and work plant.

Parasitic contamination of fresh vegetables and fruits sold in open-air markets in peri-urban areas of Jimma City, Oromia, Ethiopia: A community-based cross-sectional study.

Consuming contaminated raw vegetables and fruits is one of the primary means of parasite transmission to humans. Periodic monitoring of parasitic contamination in these food items is a crucial step in preventing the spread of parasitic disease in the community. This study was aimed at detecting intestinal parasitic contamination caused by consuming raw vegetables and fruits sold in three open-air markets and its associated factors in peri-urban areas of Jimma City, Oromia, Ethiopia. A cross-sectional study was conducted on fruits and vegetables collected from three peri-urban open-aired markets (namely; Hora Gibe, Bore and Jiren markets) in peri-urban areas of Jimma City between July and September 2021. A total of 187 fresh vegetable samples and 188 fruits were collected and examined for intestinal parasite contamination. About 200g of fruit and vegetable samples were processed and examined microscopically for parasite contamination, utilizing direct wet mount and modified Zeihl-Neelson staining methods in accordance with standard protocols. A structured questionnaire was used to collect data on the socio-demographic characteristics of vendors and risk factors for fruit and vegetable contamination. All data were analyzed using SPSS version 20.0. Of the 187 fresh vegetable samples and 188 fresh vegetable samples, 105 (56.1%) and 68/188 (36.2%) of vegetables and fruit samples, respectively, were found contaminated with one or more intestinal parasites. Remarkably, high level of contamination in fresh vegetable samples was recorded both in Carrot (Daucus carota) 63.8% (30/46) and Lettuce (Lactuca sativa) 63.1% (29/46) while Green pepper (Capsicum spp.) is the least contaminated. In fruit samples, Avokado (Persea americana) 42.6% (20/47) and Banana (Musa acuminata) 14.9% (7/47) were the most and the least commonly contaminated items respectively. The identified helminthes and protozoans were Ascaris lumbricoides, Strongyloides stercoralis, Hymenolepis nana, Entamoeba histolytica/dispar, Giardia lamblia, Cryptosporidium spp., Toxocara spp. And Fasciola spp. The most predominant parasite encountered was A. lumbricoides 46(12.3%) whereas both Toxocara spp. 12(6.9) and Fasciola spp. 2(0.5) were the least detected parasites. It is worth-mentioned that the rate of contamination in Bore market (38.15%) was higher compared with Jiren market (34.7%) and Hora Gibe market (27%). However, the rate of contamination in vegetables and fruit obtained from the three district was non-significant (p = 0.19). Contamination was more common in vegetables than fruits (AOR = 5.78, p<0.001). It was also observed that decreased parasitic contamination was significantly associated with washing the products before displaying it for selling (p < 0.001). The study has identified a high rate of raw vegetables and fruits contaminated with intestinal helminthes and protozoan. Contaminated fresh vegetables and fruits in open-aired peri-urban markets of Jimma city, Ethiopia may play a significant role in transmission of intestinal parasitic infections to humans, particularly A. lumbricoides infection. Therefore, it is urgently needed for health authorities to educate the public on the proper handling of vegetables and fruits prior to consumption.

Characterization of the serosal cells surrounding Cotesia kariyai larvae and their role in host immunosuppression

About half of the serosal cells (Scs) of Cotesia kariyai (Ck) eggs are released as teratocytes into the host body cavity after hatching, and another half remain attached to the larval epidermis until the 1st instar larvae of Ck ecdysis to 2nd instars. To investigate the role of the serosal cells surrounding Ck 1st instar larvae (1st Scs) in immune avoidance, Ck 1st instar larvae with and without Scs removed using dispase were transplanted into Mythimna separata larvae (MsLrv), respectively. As a result, Ck 1st instar larvae surrounded by Scs were less susceptible to the MsL encapsulation than Ck 1st instar larvae without the Scs, suggesting that the Scs are involved in suppressing the encapsulation of the MsL. Furthermore, when the granular cells and plasmatocytes of the MsL involved in the encapsulation were incubated in a medium supplemented with proteins extracted from 1st Scs, the plasmatocytes failed to adhere to glass slides, and did not spread their filopodium and lamellipodium. These findings suggest that 1st Scs express proteins that inhibit filopodium and lamellipodium spreading to prevent the MsL plasmatocytes from adhering to Ck larvae.

Particle removal from solid surfaces via an impinging gas jet pulse: Comparison between experimental and CFD-DEM modeling results

Computational and experimental studies are performed to investigate the influence of a gas jet pulse impinging perpendicularly onto a flat solid surface seeded with a monolayer of spherical particles. A numerical resuspension model is derived to predict particle release into the gas phase during jet impingement. To this end, discrete particles are immersed in a continuous gas phase modeled via Large Eddy Simulation to capture the effect of jet turbulence on the particle detachment process. Two-way coupling between particulate and gas phase is established via a near-wall particle drag model and a lift model. Direct particle–wall interactions are captured with adhesion, rolling friction and sliding friction models. To validate the overall modeling approach, numerical results are compared with resuspension experiments for monodisperse polystyrene particles placed on a glass slide. Simulations show that the particles preferentially mobilize by rolling, followed to a limited extend by lift off from the solid surface driven by aerodynamic forces and particle–particle collisions. Resuspension occurs in the first instants after jet impingement. Computational and experimental results for removal efficiency Γ are in good agreement in terms of the location of their r50 parameter, i.e., the radial position where 50% of the particles have been removed by the jet; both results show a linear dependence between the r50 value and the jet Reynolds number of the impinging jet. However, experimental Γ(r) curves generally have a smooth sigmoidal shape whereas numerical results predict a sharp transition. Some model shortcomings are identified which lead to an underprediction of particle lift-off and which explain the observed differences. Furthermore, the experimental Γ curves nearly collapse onto each other when plotted over the predicted local wall-shear stress.

Rapid Characterization of Phospholipids from Biological Matrix Enabled by Indium Tin Oxide (ITO) Coated Slide Assisted Enrichment MALDI Mass Spectrometry

AbstractLipidomic analysis of human serum is essential to monitor the individual's health status. Herein, we develop a facile strategy for rapid characterization of phospholipids in human serum via indium tin oxide (ITO) coated glass slide solid phase extraction MALDI mass spectrometry (ITO‐SPE‐MALDI‐MS). Phospholipid species are retained on ITO slide via solid phase extraction owing to the unique property of the ITO material; the measurement of phospholipid species from 1 μl human serum within 2 min is achievable. A comparison of ITO‐SPE strategy with conventional extraction methods was further carried out using liquid chromatography‐mass spectrometry (LC‐MS) and ion‐mobility mass spectrometry (IM‐MS), resulting in a comparable enrichment performance for the phospholipid analysis. Furthermore, rapid lipidomic profiling of serum samples from human colorectal cancer patients and cell lines was demonstrated. Our results indicate that ITO‐SPE‐MALDI‐MS provides a higher throughput strategy for the analysis of phospholipid species in complex biological mixtures, showcasing its potential for applications in the analysis of clinical biofluids.

Determination of carbamazepine in fingerprints: a feasibility study to evaluate adherence in epilepsy patients.

Background: Fingerprint drug concentrations can be used as a noninvasive and convenient alternative to evaluate adherence to pharmacotherapy. Methods: Fingerprints were applied over glass slides, extracted and analyzed by ultra-high performanceLC-MS/MS. The assay and drug adherence questionnaires were applied to 30 epilepsy patients. Results: The assay had linearity in the range 0.05-10ng fingerprint-1, with precision of 2.16-7.9% and accuracy of 95.0-102.8%. Carbamazepine (CBZ) levels in fingerprints were stable at 45°C for 15days. Concentrations in patient samples were 0.06-9.28ng fingerprint-1. A significant difference (p=0.003) was found between CBZ concentrations in fingerprints between patient groups divided as low and medium/high adherence. Conclusion: This method can potentially be applied to the identification of epilepsy patients with low adherence to CBZ pharmacotherapy.

Single Cell Analysis of Proteoforms.

We introduce single cell Proteoform imaging Mass Spectrometry (scPiMS), which realizes the benefit of direct solvent extraction and MS detection of intact proteins from single cells dropcast onto glass slides. Sampling and detection of whole proteoforms by individual ion mass spectrometry enable a scalable approach to single cell proteomics. This new scPiMS platform addresses the throughput bottleneck in single cell proteomics and boosts the cell processing rate by several fold while accessing protein composition with higher coverage.

From Wet Mount to Nucleic Acid Amplification Techniques: Current Diagnostic Methods and Future Perspectives Based on Patenting of New Assays, Stains, and Diagnostic Images for Trichomonas vaginalis Detection

Trichomoniasis is the most common non-viral sexually transmitted infection (STI) in the world. The estimated global prevalence in 2016 was 156 million adults aged 15–49. However, these data are underestimated, since the most used diagnostic method is the wet mount, which has low sensitivity, the information regarding the estimated duration of infection is limited and there is evidence of undiagnosed asymptomatic cases in both sexes. Currently 80% of cases—including both sexes—are asymptomatic, which makes the disease silent and chronic in course, leading to complications. The aim of this review was to discuss the diagnostic methods for T. vaginalis detection that are currently available and applicable in the clinical laboratory routine. Overall, nucleic acid amplification techniques are the best option for T. vaginalis detection, with higher sensitivity and specificity than other tests. Although these techniques present higher cost, their implementation should be supported to ensure correct trichomoniasis diagnosis and treatment beyond contributing to questions on epidemiology and control.

Stability enhancement of perovskite solar cells using multifunctional inorganic materials with UV protective, self cleaning, and high wear resistance properties

Organometal halide perovskite solar cells have reached a high power conversion efficiency of up to 25.8% but suffered from poor long-term stability against environmental factors such as ultraviolet irradiation and humidity of the environment. Herein, two different multifunctional transparent coatings containing AZO and ZnO porous UV light absorbers were employed on the front of the PSCs. This strategy is designed to improve the long-term stability of PSCs against UV irradiation. Moreover, the provided coatings exhibit two additional roles, including self-cleaning and high wear resistance. In this regard, AZO coating showed higher wear resistance compared to the ZnO coating. The photocatalytic self-cleaning properties of these prepared coatings make them stable against environmental pollutants. Furthermore, appropriate mechanical properties such as high hardness and low coefficient of friction that leads to high resistance against wear are other features of these coatings. The devices with AZO/Glass/FTO/meso-TiO2/Perovskite/spiro/Au and ZnO/Glass/FTO/meso-TiO2/Perovskite/spiro/Au configurations maintained 40% and 30% of their initial performance for 100 h during 11 days (9 h per day) against the UV light with the high intensity of 50 mW cm-2 which is due to higher absorption of AZO compared with ZnO in the ultraviolet region. Since AZO has a higher light transmission in the visible region in comparison to ZnO, perovskite cells with AZO protective layers have higher efficiency than perovskite cells with ZnO layers. It is worth noting that the mentioned features make these coatings usable for cover glass in all types of solar cells.

FIRST REPORT OF CURVULARIA LUNATA AND ALTERNARIA ALTERNATA CAUSING LEAF BLIGHTS ON TOMATOES IN SINDH, PAKISTAN

The tomato is an economically important crop that grows worldwide. The numerous fungal pathogens attacking tomato crops and causing severe diseases lead to yield loss. A few studies conducted regarding the identification of tomato fungal pathogens in Pakistan. However, no report was found to identify the fungal pathogens of tomato crops grown in Sindh. This study aimed to isolate, identify and characterize the tomato fungal pathogens in District Kamber Shahdadkot. Subsequently, thirty diseased tomato plant samples (leaves &amp; stems) were collected from distinct villages of Taluka Kamber District Kamber Shahdadkot. These samples were collected in polythene bags and marked with symbols like S1, S2 and so on (S=Sample). All samples were brought into Botany Department lab and CBC Shah Abdul Latif University Khairpur. PDA media was prepared, sterilized and poured into petri plates. Prior to the inoculation, pieces from samples were soaked in a 1% solution of sodium hypochlorite (NaOCl) for a minute. The petri plates were inoculated separately and incubated at natural room temperature (260C to 280C) for arising and growth. Three days later, the inoculation site manifests signs and symptoms of fungal development. Within a week fungus reached at preferable growth and spores were formed. Two slides from each petriplate were prepared i. e. one from the center of the cultures and other from the margins of the cultures. In order to finish this application, slide-sized scotch tape was cut up and immersed on the surface of cultures gently. The off cuts of the scotch tap introduced the fungal materials (mycelia and spores), which were pressed with love to the glass slides and observed. The fungi identification was made by using applications of morphological characteristics like morphology of the cultures, nature, and type of the mycelium, the shape of spores, and the color of the spores. Following these characters two fungal species were identified i. e. Curvularia lunata and Alternaria alternata

Automated Life Stage Classification of Malaria Using Deep Learning

INTRODUCTION: Malaria, an infectious illness spread by mosquitoes, is a serious hazard to humans and animals, with an increasing number of cases recorded yearly. Prompt and precise diagnosis, as well as preventative actions, are critical for effectively combating this condition. Malaria is now diagnosed using standard techniques. Microscopy of blood smears, which consists of small pictures, is used by trained specialists to identify diseased cells and define their life phases. The World Health Organisation (WHO) has approved this microscopy-based malaria diagnostic method. Drawing a blood sample from the finger, pricking it, spreading it onto a clean glass slide, and allowing it to dry naturally are all steps in the method. Thin blood smears were previously used to identify parasites under the microscope, but thick blood smears are utilized when parasite levels are low.&#x0D; OBJECTIVES: Due to its reliance on medical knowledge, high prices, time-consuming nature, and unsatisfactory outcomes, this technique has significant disadvantages. However, as deep learning algorithms progress, these activities may be completed more effectively and with fewer human resources.&#x0D; METHODS: This study demonstrates the usefulness of transfer learning, a type of deep learning, in categorizing microscopic pictures of parasitized versus uninfected malaria cells. Six models were evaluated using the publicly accessible NIH dataset, proving the usefulness of the suggested technique.&#x0D; RESULTS: VGG19 model fared better than its competitors, obtaining 95.05% accuracy, 92.83% precision, 96.88% sensitivity, 93.46% specificity, and 94.81% F1-score.&#x0D; CONCLUSION: This categorization of malaria cell photos will benefit microscopists in particular, as it will improve their workflow and provide a viable alternative for detecting malaria using microscopic cell images.

Identification of Blastocystis spp. in Urban Rodents of Different Districts in Southwestern Iran: Subtype Distribution and Possible Zoonotic Potential.

Rodents are one of the most abundant and diverse species of mammals and have recently been identified as carriers of numerous human pathogens. The current study was conducted to assess the prevalence, subtype (STs) distribution, and zoonotic potential of Blastocystis spp. in various species of rodents in Shiraz, southwestern Iran. For this aim, a total of 120 fresh fecal samples were collected from Mus musculus (n = 40), Rattus norvegicus (n = 40), and Rattus rattus (n = 40) in various municipality districts of Shiraz (6 out of 10 districts) between February and November 2020. Upon detecting parasites using light microscopy, a DNA fragment of the Blastocystis SSU rDNA gene was amplified using conventional PCR. By employing direct wet mount examination, 8 out of 120 fecal samples (6.7%; 2 from house mice, 3 from black rats, and 3 from brown rats) tested positive. Similarly, 5% (2/40) of house mice, 7.5% (3/40) of black rats, and 7.5% (3/40) of brown rats tested positive using the molecular method. Phylogenetic analysis revealed that the Blastocystis infecting different rodent species in Shiraz belonged to two potentially zoonotic STs (ST1 and ST4). Accordingly, rodents should not be overlooked as potential reservoirs of zoonotic Blastocystis infections. Different sampled urban districts and their statistical association with reported prevalence rates were analyzed separately. Overall, the issue of the frequency and ST distribution of Blastocystis in urban rodents of Iran is still open to question and for a proper understanding, wider and more comprehensive studies are needed.