Divis Laboratories Ltd.

Environmental DNA (eDNA) is transforming the way aquatic ecosystems are monitored and managed by scientists, resource managers, ENGOs, First Nations communities, and citizen scientists alike. However, available sampling systems currently don't allow for combined high filtration volumes, rapid sample collection, and preservation in the field, thus far hindering broad scale eDNA studies in the ocean specifically for small and medium scale organizations. To overcome these challenges, several modular water sampling systems that utilize hollow‐membrane (HM) filtration cartridges were developed by RKS laboratories and tested by the Fisheries and Oceans, Canada, Molecular Genetics Laboratory. Compared to Sterivex filters, an industry standard for eDNA filtration, the HM filtration cartridges allowed for a six‐fold increase in filtration volume and threefold increase in filtration speed. The field sampling systems, which combine pumps, a programmable controller, an air pump, an ozone generator, and up to eight filters at once, enabled efficient direct eDNA filtration from diverse aquatic environments, from creeks to the open ocean. To evaluate ease of deployment, we present the results of a 3 day workshop where technical staff of an Indigenous resource management organization, without any prior knowledge in eDNA sampling, were trained and performed independent eDNA sample collection. The samples were analyzed by metabarcoding and qPCR to reveal the distributions of salmon and other species co‐occurring in salmon ecosystems, from large ephemeral predators, to the planktonic prey of salmon, even including their pathogens. In this example study, we further observed a substantial shift in community composition in the vicinity of aquaculture facilities where marine species associated with aquaculture feed were detected in freshwater at high relative abundance. This study demonstrates how these sampling systems provide an efficient entry point for small and medium scale organizations to utilize eDNA to fulfill their research and monitoring objectives.

This is a pilot study conducted to validate the intensity of immunosuppression that an individual with kidney transplant develops post-surgical grafting of the organ. It also entails the plausible clinical and pharmacological factors that can contribute to the rejection of the organ on a broader scale. The immunosuppression drug under research is Tacrolimus (FK506), that is assayed for its inhibition of Calcineurin Phosphatase Activity (CPA/CaN Activity) resulting in acceptance and stabilization of the organ system as a whole after transplant. This study also attempts to prescribe a dose regimen by estimating the bioavailability of the oral dosage form. The subjects participating in this trial are an all-male group and are studied for a period of 3–6 months immediately after the surgical transplantation procedure. Therefore, the initial results obtained with the procedures followed are potential for a cohort study (of all genders and age groups).

This is a pilot study conducted to validate the intensity of immunosuppression that an individual with kidney transplant develops post-surgical grafting of the organ. It also entails the plausible clinical and pharmacological factors that can contribute to the rejection of the organ on a broader scale. The immunosuppression drug under research is Tacrolimus (FK506), that is assayed for its inhibition of Calcineurin Phosphatase Activity (CPA/CaN Activity) resulting in acceptance and stabilization of the organ system as a whole after transplant. This study also attempts to prescribe a dose regimen by estimating the bioavailability of the oral dosage form. The subjects participating in this trial are an all-male group and are studied for a period of 3-6 months immediately after the surgical transplantation procedure. Therefore, the initial results obtained with the procedures followed are potential for a cohort study (of all genders and age groups).

This paper elaborates on the biochemical nature of an IgG in a low or deionized environment. It has comparisons with two extremes of ionic strength, one is the Dulbecco’s Phosphate Buffer Saline (DPBS) and the other is the Deionised water (DIW). The experimentation performed is a prerequisite for orientation and immobilization of the IgG by exploiting its dipolar nature. However, no electric field is used in this setup, but the functionality of Ab-Ag interaction in respective media is emphasized. An additional epoxy layer has been used as support matrix to hold the capture IgG molecules, and also to understand its survival in a non-ionic atmosphere. A non-competent site directed assay is chosen, a mathematical estimate of the fluorescent endpoint can be analyzed and minimize the sample preparation time. The device built, is a step towards miniaturized immunosensor and a microarray is designed with improvisations for better signal and noise estimations. Therefore, the substrate developed is portable and aids quick analysis of multiple samples on microprinted platform.

Most of the proteins are polar by their structural configuration, their stereochemistry entails overall charge of the molecule. In this study, Immunoglobulin G (IgG) is evaluated for its dipolar nature. An exclusive immunoassay pattern is designed to validate the idea by controlling the IgG orientation with external application of the electric field (EF). It includes mathematical estimations of the torque produced and the EF strength required to orient a single IgG molecule in normal room temperatures.In current pandemic scenario, the necessity of tests that provide clinical analysis of an individual is inevitable; thereby the use of immunoassay based rapid invitro diagnostic (IVD) test devices have become the most sort after point of care devices. The device configured in this study also explains the IgG orientation and immobilization post influence of EF in two dimensional geometry of flowchannel; and how it provides a platform for detection of the analytes with higher sensitivity. Therefore, this is also an attempt towards miniaturization of biosensor and to improve the signal intensity while optimizing the signal to noise ratio (SNR). Imparting qualities that suffice a stable, robust, portable sensing platform for a biosensor remains an added objective of this research.

Background There is limited information about diabetes and thyroid related autoantibodies in children with type 1 diabetes (T1D) or their siblings in Sri Lanka. Objectives To assess in T1D children and their unaffected siblings the prevalence of autoantibodies to (1) glutamic acid decarboxylase (GADA), insulinoma associated antigen-2 (IA-2A) and zinc transporter 8 (ZnT8A) using 3 Screen ICA™ (3-Screen) and individual ELISA assays; (2) insulin (IAA); and (3) thyroid peroxidase (TPOA), thyroglobulin (TgA) and the TSH receptor (TSHRA). Methods We selected - (a) consecutive T1D children, and (b) their unaffected siblings of both sexes, from the T1D Registry at Lady Ridgeway Hospital, Colombo. Results The median age (IQR) of 235 T1D children and 252 unaffected siblings was 11 (8.4, 13.2) and 9 (5.4, 14.9) years respectively, and the duration of T1D was 23 (7, 54) months. (1) T1D children (a) 79.1% were 3-Screen positive; (b) all 3-Screen positives were individual antibody positive (GADA in 74%; IA-2A 31.1%; ZnT8A 38.7%); (c) and were younger (p=0.01 vs 3-Screen negatives); (d) multiple autoantibodies were present in 45.1%; (e) IA-2A (p=0.002) and ZnT8A (p=0.006) prevalence decreased with T1D duration. (f) TPOA and TgA prevalence was higher in T1D children compared to unaffected siblings (28%, p=0.001 and 31%, p=0.004, respectively). (2) Unaffected siblings (a) 6.3% were 3-Screen positive (p=0.001 vs T1D), and 2.4% were positive for IAA; (b) four subjects had two diabetes related autoantibodies, one of whom developed dysglycaemia during follow-up. Conclusions The 3-Screen assay, used for the first time in Sri Lankan T1D children and their siblings as a screening tool, shows a high prevalence of T1D related Abs with a high correlation with individual assays, and is also a helpful tool in screening unaffected siblings for future T1D risk. The higher prevalence of thyroid autoantibodies in T1D children is consistent with polyglandular autoimmunity.

Background Patient activation is defined as a patient’s confidence and perceived ability to manage their own health. Patient activation has been a consistent predictor of long-term health and care costs, particularly for people with multiple long-term health conditions. However, there is currently no means of measuring patient activation from what is said in health care consultations. This may be particularly important for psychological therapy because most current methods for evaluating therapy content cannot be used routinely due to time and cost restraints. Natural language processing (NLP) has been used increasingly to classify and evaluate the contents of psychological therapy. This aims to make the routine, systematic evaluation of psychological therapy contents more accessible in terms of time and cost restraints. However, comparatively little attention has been paid to algorithmic trust and interpretability, with few studies in the field involving end users or stakeholders in algorithm development. Objective This study applied a responsible design to use NLP in the development of an artificial intelligence model to automate the ratings assigned by a psychological therapy process measure: the consultation interactions coding scheme (CICS). The CICS assesses the level of patient activation observable from turn-by-turn psychological therapy interactions. Methods With consent, 128 sessions of remotely delivered cognitive behavioral therapy from 53 participants experiencing multiple physical and mental health problems were anonymously transcribed and rated by trained human CICS coders. Using participatory methodology, a multidisciplinary team proposed candidate language features that they thought would discriminate between high and low patient activation. The team included service-user researchers, psychological therapists, applied linguists, digital research experts, artificial intelligence ethics researchers, and NLP researchers. Identified language features were extracted from the transcripts alongside demographic features, and machine learning was applied using k-nearest neighbors and bagged trees algorithms to assess whether in-session patient activation and interaction types could be accurately classified. Results The k-nearest neighbors classifier obtained 73% accuracy (82% precision and 80% recall) in a test data set. The bagged trees classifier obtained 81% accuracy for test data (87% precision and 75% recall) in differentiating between interactions rated high in patient activation and those rated low or neutral. Conclusions Coproduced language features identified through a multidisciplinary collaboration can be used to discriminate among psychological therapy session contents based on patient activation among patients experiencing multiple long-term physical and mental health conditions.

Corneal opacities are important causes of blindness, and their major etiology is infectious keratitis. Slit-lamp examinations are commonly used to determine the causative pathogen; however, their diagnostic accuracy is low even for experienced ophthalmologists. To characterize the “face” of an infected cornea, we have adapted a deep learning architecture used for facial recognition and applied it to determine a probability score for a specific pathogen causing keratitis. To record the diverse features and mitigate the uncertainty, batches of probability scores of 4 serial images taken from many angles or fluorescence staining were learned for score and decision level fusion using a gradient boosting decision tree. A total of 4306 slit-lamp images including 312 images obtained by internet publications on keratitis by bacteria, fungi, acanthamoeba, and herpes simplex virus (HSV) were studied. The created algorithm had a high overall accuracy of diagnosis, e.g., the accuracy/area under the curve for acanthamoeba was 97.9%/0.995, bacteria was 90.7%/0.963, fungi was 95.0%/0.975, and HSV was 92.3%/0.946, by group K-fold validation, and it was robust to even the low resolution web images. We suggest that our hybrid deep learning-based algorithm be used as a simple and accurate method for computer-assisted diagnosis of infectious keratitis.

Background Studies on a new coronavirus disease (COVID-19) show the elevation of liver enzymes and liver fibrosis index (FIB-4) independently on pre-existing liver diseases. It points to increased liver fibrogenesis during acute COVID-19 with possible long-term consequences. This study aimed to assess liver fibrosis in COVID-19 patients by serum hyaluronic acid (HA) and FIB-4. Methods The study included the acute COVID-19 group (66 patients, 50% females, mean age 58.3 ± 14.6), the post-COVID group (58 patients in 3–6 months after the recovery, 47% females, mean age 41.2 ± 13.4), and a control group (17 people, 47% females, mean age 42.8 ± 11.0). Ultrasound elastography was performed in the post-COVID and control groups. Results Sixty-five percent of the acute COVID-19 group had increased FIB-4 (> 1.45), and 38% of patients had FIB-4 ≥ 3.25. After matching by demographics, 52% of acute COVID-19 and 5% of the post-COVID group had FIB-4 > 1.45, and 29% and 2% of patients had FIB-4 ≥ 3.25, respectively. Increased serum HA (≥ 75 ng/ml) was observed in 54% of the acute COVID-19 and 15% of the post-COVID group. In the acute COVID-19 group, HA positively correlated with FIB-4, AST, ALT, LDH, IL-6, and ferritin and negatively with blood oxygen saturation. In the post-COVID group, HA did not correlate with FIB-4, but it was positively associated with higher liver stiffness and ALT. Conclusion More than half of acute COVID-19 patients had increased serum HA and FIB-4 related to liver function tests, inflammatory markers, and blood oxygen saturation. It provides evidence for the induction of liver fibrosis by multiple factors during acute COVID-19. Findings also indicate possible liver fibrosis in about 5% of the post-COVID group.

The high antimicrobial ability and low toxicity of zinc-aminoclay (ZnAC) are claimed in our previous reports. In this study, we formulate a novel hand gel based on ZnAC and Opuntia humifusa (O. humifusa) extract, which is a high moisturizing agent. The antimicrobial activity, cytotoxicity, moisturizing effect, and clinical skin irritation of the hand gel are evaluated. The hand gel with 0.5 wt.% ZnAC and 1.0 v/v% O. humifusa extract can kill more than 99% Escherichia coli (gram-negative bacteria) and Staphylococcus aureus (gram-positive bacteria) after 24 h. Toxicity evaluation shows that, the hand gel does not affect the viability of mammalian HaCaT cells. Additionally, skin moisture is increased by applying the hand gel while its viscosity is at the standard level of commercial products. The hand gel has a skin irritation index of 0.0 and is classified as a non-irritating product. We successfully formulated hand gel from ZnAC, glucomannan, glycerol, and O. humifusa extract. Owing to the high antimicrobial activity and skin protection of hand gels, they are suitable to be used as hand sanitizers in restaurants, hospitals, and homes effectively.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Corneal opacities are an important cause of blindness, and its major etiology is infectious keratitis. Slit-lamp examinations are commonly used to determine the causative pathogen; however, their diagnostic accuracy is low even for experienced ophthalmologists. To characterize the “face” of an infected cornea, we have adapted a deep learning architecture used for facial recognition and applied it to determine a probability score for a specific pathogen causing keratitis. To record the diverse features and mitigate the uncertainty, batches of probability scores of 4 serial images taken from many angles or fluorescence staining were learned for score and decision level fusion using a gradient boosting decision tree. A total of 4306 slit-lamp images and 312 images obtained by internet publications on keratitis by bacteria, fungi, acanthamoeba, and herpes simplex virus (HSV) were studied. The created algorithm had a high overall accuracy of diagnosis, e.g., the accuracy/area under the curve (AUC) for acanthamoeba was 97.9%/0.995, bacteria was 90.7%/0.963, fungi was 95.0%/0.975, and HSV was 92.3%/0.946, by group K-fold validation, and it was robust to even the low resolution web images. We suggest that our hybrid deep learning-based algorithm be used as a simple and accurate method for computer-assisted diagnosis of infectious keratitis.

Sequence variants (SV) in protein bio therapeutics can be categorized as unwanted impurities and may raise serious concerns in efficacy and safety of the product. Early detection of specific sequence modifications, that can result in altered physicochemical and or biological properties, is therefore desirable in product manufacturing. Because of their low abundance, and finite resolving power of conventional analytical techniques, they are often overlooked in early drug development. Here, we present a case study where trace amount of a sequence variant is identified in a monoclonal antibody (mAb) based therapeutic protein by LC–MS/MS and the structural and functional features of the SV containing mAb is assessed using appropriate analytical techniques. Further, a very sensitive selected reaction monitoring (SRM) technique is developed to quantify the SV which revealed both prominent and inconspicuous nature of the variant in process chromatography. We present the extensive characterization of a sequence variant in protein biopharmaceutical and first report on control of sequence variants to < 0.05% in final drug product by utilizing SRM based mass spectrometry method during the purification steps.

The objective of this study is to develop a hybrid model by combining physics and data-driven approach for optimum unconventional field development. We used physics-based reservoir simulations to generate training datasets. These uncalibrated priors were incorporated into data-driven machine learning (ML) algorithms so that the algorithms can learn the underlying physics between reservoir simulation input and output, cumulative oil production for parent and child wells. The reservoir simulations in a single half-cluster model consists of injection and production phases. This allows the algorithm to relate the impact of completion design, well spacing and timing to the production profiles. After performing a sensitivity analysis to reduce the number of training inputs, more than 20,000 simulations results were generated as the training data. The best accuracy, R² = 0.94, was achieved with the neural network model after tuning hyper-parameters. Then, we incorporated the hybrid model with the genetic algorithm to perform efficient history matching to calibrate model parameters and predict estimated ultimate recovery (EUR) and net present value with 10% discount rate (NPV10). The great efficiency in the hybrid model takes only several minutes to complete a single well history matching. The calibrated model shows that the prediction from the hybrid model is physically meaningful compared to actual reservoir simulations, capturing the impact of fracture geometry, child well spacing and timing on the well production. With multiple history matching results, we populated value acreage maps (e.g., EUR and NPV10) which can benefit the unconventional field development planning. Lastly, a blind test was conducted in an area of interest to demonstrate that the proposed workflow can effectively predict a well performance in the area without sufficient data, utilizing calibrated model parameters from history matched results of adjacent wells. The proposed model can provide quick and scalable solutions that honor underlying physics to help decision making on unconventional field development based on production profile and economic metrics with various completion designs.

Background: Strontium ranelate (StR) is an antiosteoporotic agent previously utilized for the enhancement of fracture union. We investigated the effects of StR on fracture healing using a rabbit model. Methods: Forty adult female rabbits were included in the study and were divided in 2 equal groups, according to StR treatment or untreated controls. All animals were subjected to osteotomy of the ulna, while the contralateral ulna remained intact and served as a control for the biomechanical assessment of fracture healing. Animals in the study group received 600 mg/kg/day of StR orally. All animals received ordinary food. At 2 and 4 weeks, all animals were euthanatized and the osteotomy sites were evaluated for healing through radiological, biomechanical, and histopathological studies. Results: The treatment group presented statistically significant higher callus diameter, total callus area, percentage of fibrous tissue (p < 0.001), vessels/mm2, number of total vessels, and lower osteoclast number/mm2 (p < 0.05) than the control group at 2 weeks. Additionally, the treatment group presented significantly higher percentages of new trabecular bone, vessels/mm2, osteoclast number/mm2, and lower values for callus diameter, as well as total callus area (p < 0.05), than the control group at 4 weeks. At 4 weeks, in the treatment group, force applied (p = 0.003), energy at failure (p = 0.004), and load at failure (p = 0.003) were all significantly higher in the forearm specimens with the osteotomized ulnae compared to those without. Radiological bone union was demonstrated for animals receiving StR at 4 weeks compared with controls (p = 0.045). Conclusion: StR appears to enhance fracture healing but further studies are warranted in order to better elucidate the mechanisms and benefits of StR treatment.

Studies on the TSH receptor (TSHR) have numerous practical applications in vitro and in vivo. For example human monoclonal autoantibodies (MAbs) to the TSHR are useful reagents for in vitro diagnostics. Measurement of TSHR autoantibodies (TRAbs) is helpful in diagnosis and management of autoimmune thyroid disease. Currently available highly sensitive and specific assays to measure TRAbs use the human TSHR MAb M22 instead of the TSH. Furthermore, preparations of the human TSHR MAb M22 are useful as the World Health Organisation International Standard for thyroid stimulating antibody and for calibration of the assays for measuring TRAbs. Preparations of thermostabilised TSHR extracellular domain have recently become available and this is likely to have an impact on improvements in specificity testing for TRAb assays. In addition the stable TSHR preparations have practical application for specific immunoadsorption of patient serum TRAbs. Human TSHR MAbs also have promising prospects as new therapeutics. Autoantibodies with TSHR antagonistic activities are “natural” inhibitors of TSHR stimulation and are expected to be helpful in controlling TSHR activity in patients with Graves’ disease, Graves’ ophthalmopathy and thyroid cancer.

Pacific oyster Crassostrea gigas, endemic to coastal Asia, has been translocated globally throughout the past century, resulting in self‐sustaining introduced populations (naturalized). Oyster aquaculture industries in many parts of the world depend on commercially available seed (hatchery‐farmed) or naturalized/wild oysters to move onto a farm (naturalized‐farmed). It is therefore important to understand genetic variation among populations and farm types. Here we genotype naturalized/wild populations from France, Japan, China, and most extensively in coastal British Columbia, Canada. We also genotype cultured populations from throughout the Northern Hemisphere to compare with naturalized populations. In total, 16,942 markers were identified using double‐digest RAD‐sequencing in 182 naturalized, 112 hatchery‐farmed, and 72 naturalized‐farmed oysters (n = 366). Consistent with previous studies, very low genetic differentiation was observed around Vancouver Island (mean FST = 0.0019), and low differentiation between countries in the Japan‐Canada‐France historical translocation lineage (France‐Canada FST = 0.0024; Japan‐Canada FST = 0.0060). Chinese populations were more differentiated (China‐Japan FST = 0.0241). Hatchery‐propagated populations had higher inter‐individual relatedness suggesting family structure. Within‐population inbreeding was not detected on farms, but nucleotide diversity and polymorphism rate was lower in one farm population. Moving oysters from nature onto farms did not result in strong within‐generation selection. Private alleles at substantial frequency were identified in several hatchery populations grown in BC, suggesting non‐local origins. Tests of selection identified outlier loci consistent with selective differences associated with domestication, in some cases consistently identified in multiple farms. Top outlier candidates were nearby genes involved in calcium signaling and calmodulin activity. Implications of potential introgression from hatchery‐farmed oysters depends on whether naturalized populations are valued as a locally‐adapted resource or as an introduced, invasive species. Given the value of the industry in BC and the challenges the industry faces (e.g., climate change, crop losses, biotic stressors), this remains an important question.

Salivary gland neoplasms are a morphologically heterogenous group of lesions that are often diagnostically challenging. In recent years, considerable progress in salivary gland taxonomy has been reached by the discovery of tumor type-specific fusion oncogenes generated by chromosome translocations. This review describes the clinicopathologic features of a selected group of salivary gland carcinomas with a focus on their distinctive genomic characteristics. Mammary analog secretory carcinoma is a recently described entity characterized by a t(12;15)(p13;q25) translocation resulting in an ETV6-NTRK3 fusion. Hyalinizing clear cell carcinoma is a low-grade tumor with infrequent nodal and distant metastasis, recently shown to harbor an EWSR1-ATF1 gene fusion. The CRTC1-MAML2 fusion gene resulting from a t(11;19)(q21;p13) translocation, is now known to be a feature of both low-grade and high-grade mucoepidermoid carcinomas associated with improved survival. A t(6;9)(q22-23;p23-34) translocation resulting in a MYB-NFIB gene fusion has been identified in the majority of adenoid cystic carcinomas. Polymorphous (low-grade) adenocarcinoma and cribriform adenocarcinoma of (minor) salivary gland origin are related entities with partly differing clinicopathologic and genomic profiles; they are the subject of an ongoing taxonomic debate. Polymorphous (low-grade) adenocarcinomas are characterized by hot spot point E710D mutations in the PRKD1 gene, whereas cribriform adenocarcinoma of (minor) salivary glands origin are characterized by translocations involving the PRKD1-3 genes. Salivary duct carcinoma (SDC) is a high-grade adenocarcinoma with morphologic and molecular features akin to invasive ductal carcinoma of the breast, including HER2 gene amplification, mutations of TP53, PIK3CA, and HRAS and loss or mutation of PTEN. Notably, a recurrent NCOA4-RET fusion has also been found in SDC. A subset of SDC with apocrine morphology is associated with overexpression of androgen receptors. As these genetic aberrations are recurrent they serve as powerful diagnostic tools in salivary gland tumor diagnosis, and therefore also in refinement of salivary gland cancer classification. Moreover, they are promising as prognostic biomarkers and targets of therapy.