Glass Slides Research Articles

The 3-billion fossil question: How to automate classification of microfossils

Microfossil classification is an important discipline in subsurface exploration, for both oil & gas and Carbon Capture and Storage (CCS). The abundance and distribution of species found in sedimentary rocks provide valuable information about the age and depositional environment. However, the analysis is difficult and time-consuming, as it is based on manual work by human experts. Attempts to automate this process face two key challenges: (1) the input data are very large - our dataset is projected to grow to 3 billion microfossils, and (2) there are not enough labeled data to use the standard procedure of training a deep learning classifier. We propose an efficient pipeline for processing and grouping fossils by genus, or even species, from microscope slides using self-supervised learning. First we show how to efficiently extract crops from whole slide images by adapting previously trained object detection algorithms. Second, we provide a comparison of a range of self-supervised learning methods to classify and identify microfossils from very few labels. We obtain excellent results with both convolutional neural networks and vision transformers fine-tuned by self-supervision. Our approach is fast and computationally light, providing a handy tool for geologists working with microfossils.

A large scale bacterial attraction assay: A new quantitative bacterial migration assay suitable for genetic screens.

Bacteria use various motility mechanisms to explore their environments. Chemotaxis is the ability of a motile bacterial cell to direct its movement in response to chemical gradients. A number of methods have been developed and widely used to study chemotactic responses to chemoeffectors including capillary, agar plug, microscopic slide, and microfluidic assays. While valuable, these assays are primarily designed to monitor rapid chemotactic responses to chemoeffectors on a small scale, which poses challenges in collecting large quantities of attracted bacteria. Consequently, these setups are not ideal for experiments like forward genetic screens. To overcome this limitation, we developed the Large Scale Bacterial Attraction assay (LSBA), which relies on the use of a Nalgene™ Reusable Filter Unit and other materials commonly found in laboratories. We validate the LSBA by investigating chemoeffector kinetics in the setup and by using chemoattractants to quantify the chemotactic response of wild-type, and motility impaired strains of the plant pathogenic bacterium Xanthomonas campestris pv. campestris and the environmental bacterium Shewanella oneidensis. We show that the LSBA establishes a long lasting chemoeffector gradient, that the setup can be used to quantify bacterial migration over time and that the LSBA offers the possibility to collect high numbers of attracted bacteria, making it suitable for genetic screens.

Patterns of Use and Barriers to STI Point-of-care Tests for Military Obstetrician Gynecologists.

Sexually transmitted infections (STIs) are commonly reported in military populations. Point-of-care tests (POCTs) are commercially available, but their use is variable in the civilian sector. Their use among military providers has not been evaluated. We sought to identify the pattern of use and barriers to using STI POCTs for military obstetrician/gynecologists (OBGYNs). We adapted a survey of civilian OBGYNs on patterns of use and barriers to STI POCTs for military OBGYNs. We sent an online questionnaire to 479 military OBGYNs via Army, Air Force, and Navy specialty leaders in May 2023. The questionnaire included 14 demographic questions and up to 52 questions regarding availability, use, and barriers to STI POCTs. The USU Institutional Review Board deemed the study exempt from Institutional Review Board review. Of the 479 solicited, 117 participated in the survey (24.4%). Of respondents, 64.1% were women and 79.5% non-Hispanic white. Sexually transmitted infections were detected once to twice weekly by 13.0% of respondents and once or twice monthly by 52.8%. The most available STI-related POCTs were wet mount prep (68.7%), rapid HIV (43.3%), and urine dipstick (38.6%). Gram stain was available for 30.3%, the Affirm VPIII (Becton, Dickinson and Company, Franklin Lakes, NJ) for 24.5%, and stat RPR for 16.3%. Economic barriers to using POCTs included cost of the test from manufacturer/distributor (57.9%) and military funding/stocking decisions (10.3%). The greatest barriers to use were the purchasing of an instrument (60.8%) and the interruption to workflow in clinic (57.8%). Military OBGYNs rely on several STI-related POCTs. Economic factors and interruption to workflow were cited as the most significant barriers to using POCTs for military OBGYNs. Test cost and impact on workflow should be considered in future development and procurement of POCTs for the Military Health System.

Tailoring bistability in optical tweezers with vortex beams and spherical aberration

We demonstrate a bistable optical trap by tightly focusing a vortex laser beam. The optical potential has the form of a Mexican hat with an additional minimum at the center. The bistable trapping corresponds to a nonequilibrium steady state, where the microsphere continually hops, due to thermal activation, between an axial equilibrium state and an orbital state driven by the optical torque. We develop a theoretical model for the optical force field, based entirely on experimentally accessible parameters, combining a Debye-type nonparaxial description of the focused vortex beam with Mie scattering by the microsphere. The theoretical prediction that the microsphere and the annular laser focal spot should have comparable sizes is confirmed experimentally by taking different values for the topological charge of the vortex beam. Spherical aberration introduced by refraction at the interface between the glass slide and the sample is considered and allows us to finetune between axial, bistable, and orbital states as the sample is shifted with respect to the objective focal plane. We find overall agreement between theory and experiment for a rather broad range of topological charges. Our results open the way for applications in stochastic thermodynamics, as they establish a control parameter—the height of the objective focal plane with respect to the glass slide—that allows us to shape the optical force field in real time and in a controllable way. Published by the American Physical Society 2024

Salivary duct carcinoma with squamous differentiation: histomorphological and immunophenotypical analysis of six cases.

Salivary duct carcinoma (SDC) is an aggressive salivary malignancy with multiple morphological subtypes. Primary salivary squamous cell carcinoma (SCC) requires exclusion of high-grade salivary malignancies and metastatic disease and is considered exceptionally rare. We report six cases of SDC with resemblance to SCC on account of variable, but often extensive, squamous differentiation. A retrospective review (2009-2023) at two institutions of SDC with histological and immunophenotypical evidence of squamous differentiation identified six cases. Medical charts and available glass slides were reviewed. There were five males and one female with a median age of 63 years, with tumours involving the parotid (five of six) and submandibular (one of six) glands. All six tumours showed a conventional SDC component comprising < 5-90% of viable tumour. Squamous differentiation comprised 10-95%+ (> 75% in three of six cases) of total viable tumour, and demonstrated CK5/6, p63 and/or p40 immunoexpression in all cases. A sarcomatoid component, comprising 10-60% of viable tumour, was present in three of six (50%) cases. All tumours were androgen receptor (AR)-positive, but only two of six (33.3%) retained AR immunoreactivity in the squamous component. Metastatic SDC to regional lymph nodes exhibited exclusive squamous differentiation in two of six (33.3%) cases. Squamous differentiation, histologically and immunophenotypically, can be extensive in SDC. AR expression may be lost in the squamous component and metastases may demonstrate only squamous differentiation. These findings cast further doubt on the existence of primary salivary SCC. SDC should be considered whenever encountering a carcinoma with squamous differentiation in major salivary glands or within cervical lymph nodes in the setting of a salivary mass.

A Minimal Approach to Demonstrate Concordance of Digital and Conventional Microscopy in Toxicologic Pathology.

Digitalization of pathology workflows has undergone a rapid evolution and has been widely established in the diagnostic field but remains a challenge in the nonclinical safety context due to lack of regulatory guidance and validation experience for good laboratory practice (GLP) use. One means to demonstrate that digital slides are fit for purpose, that is, provide sufficient quality for pathologists to reach a diagnosis, is conduction of comparison studies, which have been published both, for veterinary and human diagnostic pathology, but not for toxicologic pathology. Here, we present an approach that uses study material from nonclinical safety studies and that allows for the statistical comparison of concordance rates for glass and digital slide evaluation while minimizing time and effort for the involved personnel. Using a benchmark study design, we demonstrate that evaluation of digital slides fits the purpose of nonclinical safety evaluation. These results add to reports of successful workflow validations and support the full adaptation of digital pathology in the regulatory field.

Intraflagellar transport speed is sensitive to genetic and mechanical perturbations to flagellar beating.

Two sets of motor proteins underpin motile cilia/flagella function. The axoneme-associated inner and outer dynein arms drive sliding of adjacent axoneme microtubule doublets to periodically bend the flagellum for beating, while intraflagellar transport (IFT) kinesins and dyneins carry IFT trains bidirectionally along the axoneme. Despite assembling motile cilia and flagella, IFT train speeds have only previously been quantified in immobilized flagella-mechanical immobilization or genetic paralysis. This has limited investigation of the interaction between IFT and flagellar beating. Here, in uniflagellate Leishmania parasites, we use high-frequency, dual-color fluorescence microscopy to visualize IFT train movement in beating flagella. We discovered that adhesion of flagella to a microscope slide is detrimental, reducing IFT train speed and increasing train stalling. In flagella free to move, IFT train speed is not strongly dependent on flagella beat type; however, permanent disruption of flagella beating by deletion of genes necessary for formation or regulation of beating showed an inverse correlation of beat frequency and IFT train speed.

Classification of healthy and cancerous colon cells by Fourier transform infrared spectroscopy

Colorectal cancer is one of the most diagnosed types of cancer in developed countries. Current diagnostic methods are partly dependent on pathologist experience and laboratories instrumentation. In this study, we used Fourier Transform Infrared (FTIR) spectroscopy in transflection mode, combined with Principal Components Analysis followed by Linear Discriminant Analysis (PCA-LDA) and Partial Least Squares – Discriminant Analysis (PLS-DA), to build a classification algorithm to diagnose colon cancer in cell samples, based on absorption spectra measured in two spectral ranges of the mid-infrared spectrum. In particular, PCA technique highlights small biochemical differences between healthy and cancerous cells: these are related to the larger lipid content in the former compared with the latter and to the larger relative amount of protein and nucleic acid components in the cancerous cells compared with the healthy ones. Comparison of the classification accuracy of PCA-LDA and PLS-DA methods applied to FTIR spectra measured in the 1000–1800 cm−1 (low wavenumber range, LWR) and 2700–3700 cm−1 (high wavenumber range, HWR) remarks that both algorithms are able to classify hidden class FTIR spectra with excellent accuracy (100 %) in both spectral regions. This is a hopeful result for clinical translation of infrared spectroscopy: in fact, it makes reliable the predictions obtained using FTIR measurements carried out only in the HWR, in which the glass slides used in clinical laboratories are transparent to IR radiation.

Enhanced visualization of articular cartilage chondroprogenitor-derived extracellular vesicles using cytospin centrifugation for confocal imaging

Characterizing Extracellular Vesicles (EVs) poses a challenge due to their complex composition and small size. Efforts to visualize fluorescently labeled EVs post-isolation with confocal microscopy encounter a significant obstacle in congregating the isolates on slides. While cytospin is a well-established method for cells, its application with EVs remains unexplored. This study aimed to isolate EVs and evaluate the efficiency of cytospin preparation to enhance their visualization using confocal microscopy. Following informed consent, cartilage shavings from a non-diseased human tibiofemoral joint were digested to obtain cartilage-resident chondroprogenitors through a migratory-assay (MCP). The MCPs were characterized for MSC markers (positive: CD105, CD73, CD90; negative: HLA-DR, CD34, CD45) using FACS. The conditioned medium was utilized to isolate EVs using the cutoff filter and precipitation technique, and their confirmation for transmembrane markers CD63 and CD81 was performed via FACS. Subsequently, the isolated EVs were subjected to confocal microscopy with and without (control) cytospin preparation. The MCPs exhibited high expression of positive and low expression of negative MSC markers. The study effectively employed cytospin centrifugation and confocal imaging to robustly identify EVs isolated from MCPs. Fluorescently labeled with CD63 and CD81 markers, the EVs isolated using cytospin centrifugation were concentrated on glass slides, and compared to control slides; the experimental setup facilitated a 100 times concentration of EVs, thereby enabling easy identification. Confocal analysis confirmed positive expressions of CD63 and CD81, aligning with FACS results. This study introduces a novel approach that enhances the visualization of MCP-derived EVs using cytospin centrifugation.

P‐190: Photo‐triggered Transmission‐color Through a Cholesteric Liquid Crystal for Multi‐level Information Encryption

In this research, the house‐made transparent cell with a cell gap of 10 μm was made using one glass slide that coated with commercial polyimide and the other one coated by SD1 photo‐responsive molecules, and filled with CLCs made from E7 nematic LCs and 1.0% S811 doping in the pitch of 10 μm. The LCs on SD1 molecules coated slide thereafter were in‐plane switched clock‐wisely by means of linear polarized blue laser (λ=405nm) irradiation, and thus elongate the pitch and tune reflection of CLCs. As the reflection of incident light has an extremely large wavelength (~14×103 nm) and is hard to be detected, the structure change induced optical performance in CLCs by in‐plane switch of near‐slide LCs was identified by a polarized optical microscopy (POM) under the transmission mode. The cell inserted with CLCs was saw in purple initially, when the near‐slide LCs were clock‐wisely switched by π/4, 5π/12, 7π/12, 2π/3 and 5π/6, respectively, the cell turned to indigo, green, yellow, orange and pink accordingly. Alternatively, the induced pink cells can be counter‐tuned to their initial purple by anti‐clockwise laser irradiation. This observation suggests that the switching of near‐slip LCs is sufficient for optically encoding in CLCs and could have significant applications in displays, especially in a data‐hidden mode.

A deep learning-based model for detecting Leishmania amastigotes in microscopic slides: a new approach to telemedicine

BackgroundLeishmaniasis, an illness caused by protozoa, accounts for a substantial number of human fatalities globally, thereby emerging as one of the most fatal parasitic diseases. The conventional methods employed for detecting the Leishmania parasite through microscopy are not only time-consuming but also susceptible to errors. Therefore, the main objective of this study is to develop a model based on deep learning, a subfield of artificial intelligence, that could facilitate automated diagnosis of leishmaniasis.MethodsIn this research, we introduce LeishFuNet, a deep learning framework designed for detecting Leishmania parasites in microscopic images. To enhance the performance of our model through same-domain transfer learning, we initially train four distinct models: VGG19, ResNet50, MobileNetV2, and DenseNet 169 on a dataset related to another infectious disease, COVID-19. These trained models are then utilized as new pre-trained models and fine-tuned on a set of 292 self-collected high-resolution microscopic images, consisting of 138 positive cases and 154 negative cases. The final prediction is generated through the fusion of information analyzed by these pre-trained models. Grad-CAM, an explainable artificial intelligence technique, is implemented to demonstrate the model’s interpretability.ResultsThe final results of utilizing our model for detecting amastigotes in microscopic images are as follows: accuracy of 98.95 1.4%, specificity of 98 2.67%, sensitivity of 100%, precision of 97.91 2.77%, F1-score of 98.92 1.43%, and Area Under Receiver Operating Characteristic Curve of 99 1.33.ConclusionThe newly devised system is precise, swift, user-friendly, and economical, thus indicating the potential of deep learning as a substitute for the prevailing leishmanial diagnostic techniques.

A scalable, passive sampling method for the quantification of airborne allergens

Traditionally, airborne concentrations of aeroallergens are sampled in a single location by an active sampler, which requires electricity and regular maintenance. However, aeroallergen concentrations may vary widely over urban and rural environments, requiring a method that is cost-effective and scalable so that many measurements can be made across an air shed. We developed such a method that uses passive sampling and light microscopy for analysis. Inexpensive and easy to operate, passive samplers rely on the gravitational settling of particles onto microscope slides. This determines airborne pollen concentration through: 1) sample collection using a modified Durham sampler, 2) preparation of samples for microscopy and strategic sample imaging, and 3) simplified particle measurements and calculation of pollen concentration following deposition velocity models proposed by Scheppegrell [1] and Wagner and Leith [2]. This method was verified with two sampling campaigns during the ragweed season of 2020 and the tree pollen season of 2021. The concentrations determined with the passive and Burkard sampling methods were found to be well-correlated (r > 0.99, r = 0.87) and precise (%CV = 20 %, 21 %). The validation of passive samplers will enable measurements of aeroallergens over wider spatial scales and help determine where aeroallergen exposure risks are greatest.•An inexpensive and low-cost method was developed to determine airborne pollen counts.•The method was evaluated for its accuracy and reproducibility.•The method can be applied to examine the concentrations and spatial variability of airborne pollen.

Clinicopathological study on diameter of extranodal extension of cervical metastatic lymph nodes in the prognosis of oral cancer

ObjectivesTo investigate the relationship between the degree of destruction of the cervical lymph node capsule, extranodal invasion distance, and the prognosis of extranodal extension (ENE)-positive patients Study designWe retrospectively examined microscopic slides from neck dissection specimens of ENE-positive patients of our hospital. The ENE distance was measured by a pathologist who set up a virtual lymph node and measured the maximum extranodal invasion distance. The maximum distance was used for multiple ENEs. Forty patients with ENE were enrolled in this study. The Kaplan–Meier method was used to estimate survival. ResultsAmong the ENE-positive cases, the capsule was completely destroyed and partially destroyed in seven and 33 cases, respectively. Disease-specific survival (DSS) was 1251 days (range 156–3009 days). The median distance of extranodal invasion was 2500 µm (392–8500 µm) in the 33 ENE-positive cases in which the capsule was not completely destroyed. Receiver operating characteristic curve analysis of these 33 cases showed that the cutoff value of extranodal invasion distance for progression-free survival was 2241 µm. ConclusionsENE is a prognostic predictor of oral cancer; ENE was an independent prognostic factor; and ENE size cutoff of 2241 µm was a significant prognostic factor.

P‐131: Spherical Forming‐A Design and Production of Spherical Display from 2D Plane to 3D Surface

OLED flexible displays technology has been rapidly developing, but the main lamination process of it is still in 2D status. Due to wrinkles and other issues, currently there is not much experience in mass production for the 3D lamination. In this work, we mainly designed a spherical cover glass, and realized the lamination of it and flexible displays. We also proposed a solution for wrinkles during the lamination process.

Influence of collector type and the glass cover cooling on the performance of the solar distiller integrated with the solar collectors

Improving the efficiency of solar distillers is essential to increasing freshwater production. One method to enhance the output of the solar distiller is to connect it with another solar collector. Previous studies did not indicate a comparison of the performance of integrated solar stills with different types of solar collectors. The current article aims to study the performance of solar distillers connected to two different types of solar collectors, study the influencing operational variables, and compare these cases. A practical model was built that included four operational cases. The first case (M1) was a solar heater with a solar concentrator collector and a solar distiller connected in series. The second case (M2): A solar concentrator collector and solar distiller connected in series. The third case (M3): A solar heater and solar distiller connected in series. The fourth case (M4): It is the same as the M1 system, but the solar distiller contains a tube to cool the glass and compare the productivity with the classical solar distiller. The results showed that the M1 case is higher than the M3 and M2 cases. In contrast, the M4 case had the highest productivity in all the cases and systems that were discussed, which is estimated at 7583 ml/ day; this means that the M4 system is the best system studied, and this is due to the glass cooling mechanism. The highest productivity recorded for the M4 system was on 28 June, and the lowest productivity recorded was on 15 July. The highest hourly productivity was reached when the glass surface temperature (4 ˚C) was 1400 ml/h at 14:00.

41‐2: A Patterned Packaging Scheme of MiniLED Tiled Display with HighTransmittance and High Color Consistency in Light and Dark States

Tiled display has gradually become the development direction of super large screen display. A high transmittance greater than 80% and visual consistency with ΔE&gt;0.5 in off state and Δu′v′&gt;0.004 between multiple modules in display state MiniLED tiled display packaging scheme was proposed in this paper. The LED on the display substrate was wrapped by the barrier and diffusion particles. In addition, the glass cover plate with stable OD BM pattern is pasted above the display substrate to achieve consistency of blackness between multiple modules, with diamond black effect. This scheme is of great significance to the development of tiled display technology.

A Workshop on the Utilization of Light Microscope for Biology Education Pre-Service Students of FKIP ULM through the Use of Wet Mount Preparations

Microscopes in learning biology are very important as a tool for students in studying microscopic organisms and objects that cannot be seen by the eye directly. The results of the needs analysis show that biology education students in the Year of 2022 have never received training in the use and maintenance of microscopes and have never used a microscope with a magnification of 1000x. therefore, 98% of the survey results to participants indicate the need for training in the use of microscopes. The training on the use of light microscope was trained to make wet mount preparations of Rhoeo discolor leaf stomata and Hibiscus rosa-sinensis flower pollen. The microscopes used were monocular microscope and electric binocular microscope. The microscope magnifications used were 10x10; 10x40; and 10x100. The training results show that students are able to use all microscope magnifications and figures of the results of microscope observations well and clearly. The results of the microscope proficiency test were 21.06%, very good; 45.61% good/adequate grades; 24.56 adequate grades, but there were 8.7% still getting poor grades. The next service can be trained in making preparations with the whole mount preparation method, squash method for mitosis observation, slice preparation method without embedding and slice preparation method with paraffin method.

Pediatric Urinary Tract Infections at a Tertiary Care Center: Microbial Diversity and Antibiotic Resistance Patterns

Abstract Introduction: Urinary tract infection (UTI) remains a prevalent bacterial infection among the pediatric age group, ranking as the third-most common bacterial infection in children in developing countries, following gastrointestinal and respiratory tract infections. It continues to pose a significant health challenge. Materials and Methods: The urine samples underwent gross examination, wet mount, and Gram stain. Semiquantitative cultures were conducted on conventional media (MacConkey agar, blood agar, and CLED agar) and UTI chromogenic media. Uropathogen identification employed standard microbiological techniques. Antibiotic susceptibility was determined using the Kirby–Bauer disk diffusion method, with interpretation based on CLSI guidelines. Plates were incubated overnight, and clear zone diameters around antibiotic discs were measured for sensitivity or resistance determination. Results: The study comprised 64.75% male children and 35.25% female children. Analyzing the age distribution, the majority of participants fell within the age range of 1–5 years (35%), followed by those &lt;1 year (33.75%), and the age group of 5–12 years, accounting for 31.25% of the total 400 participants. The findings from our investigation revealed a UTI prevalence of 17.25%, with Escherichia coli and Klebsiella emerging as the predominant uropathogens. Notably, these pathogens exhibited a significant susceptibility to carbapenems, nitrofurantoin, and amikacin. Conclusion: Our study identified a male predominance and various age distributions among UTI patients. Antibiotic susceptibility patterns revealed E. coli and Klebsiella pneumoniae’s high sensitivity to key antibiotics, whereas Enterococcus spp. exhibited significant high-level aminoglycoside resistance. This study underscores the importance of tailored antibiotic strategies based on local resistance profiles to combat UTIs effectively.

Shedding more light on shedders

We report on testing 100 individuals for their shedder status with the aim of demonstrating whether the process of cell staining is reproducible when testing a large number of people. A previous report using the same method was based on 11 donors and indicated that there may be a continuum of shedder types within this small sample set. In this report we also expand the time points post-handwashing to 0, 15, 30, 60, and 180 min. Triplicate samples were collected from both the right and left thumbs. Samples were collected by donors placing a thumb on a clean glass slide and then adding a DNA binding dye. The number of cells were recorded within three separate square millimetre areas (cells/mm2) at 220x magnification. The experiments were conducted in triplicate on three different days, giving a total of 72 thumbprints per individual. Finally, there were 3438 observed frames in the entire dataset. Of the 100 donors, 98 gave consistent and reproducible cell number deposition. There was no difference between the cells deposited by the left and right thumbs in 13 of 15 tested. Males tended to deposit more cells than females. If applying arbitrary boundary to a cell count to definitively determine shedder status, then many of the donors fell within two categories. This study based on 100 individuals strongly suggests that shedder status is a continuum phenomenon.

Detection of milk adulteration using coffee ring effect and convolutional neural network

A low-cost and effective method is reported to identify water and synthetic milk adulteration of cow’s milk using coffee ring patterns. The cow’s milk samples were diluted with tap water (TW), distilled water (DW) and mineral water (MW) and drop cast onto glass slides to observe coffee ring patterns. The area of the ring, total particle area and average particle diameter were extracted from these patterns. For each ring, the ratio of total particle area versus total ring area was calculated. The area ratio, regardless of water adulterants, follows an exponential model with respect to average particle diameter. Unlike TW, the ratio for DW and MW adulterated milk are clustered and classified together with respect to the particle diameter. These results were independent of dilution level and are used for adulterant classification. The ring of milk adulterated using synthetic milk gave multiple concentric rings, flower-like structures, and oil globules throughout the dilution level. An Alexnet model was used to classify water and synthetic milk adulterants in authentic milk. The trained model could achieve 96.7% and 95.8% accuracy for binary and tertiary classification respectively. These results enable us to distinguish synthetic milk from pure milk and segregate DW and MW with respect to TW adulterated milk.