Training and validation of a novel non-invasive imaging system for ruling out malignancy in canine subcutaneous and cutaneous masses using machine learning in 664 masses.

Objective: To train and validate the use of a novel artificial intelligence-based thermal imaging system as a screening tool to rule out malignancy in cutaneous and subcutaneous masses in dogs. Animals: Training study: 147 client-owned dogs with 233 masses. Validation Study: 299 client-owned dogs with 525 masses. Cytology was non-diagnostic in 94 masses, resulting in 431 masses from 248 dogs with diagnostic samples. Procedures: The prospective studies were conducted between June 2020 and July 2022. During the scan, each mass and its adjacent healthy tissue was heated by a high-power Light-Emitting Diode. The tissue temperature was recorded by the device and consequently analyzed using a supervised machine learning algorithm to determine whether the mass required further investigation. The first study was performed to collect data to train the algorithm. The second study validated the algorithm, as the real-time device predictions were compared to the cytology and/or biopsy results. Results: The results for the validation study were that the device correctly classified 45 out of 53 malignant masses and 253 out of 378 benign masses (sensitivity = 85% and specificity = 67%). The negative predictive value of the system (i.e., percent of benign masses identified as benign) was 97%. Clinical relevance: The results demonstrate that this novel system could be used as a decision-support tool at the point of care, enabling clinicians to differentiate between benign lesions and those requiring further diagnostics.

The Chromosome Counts Database (CCDB).

For decades, plant biologists have been interested in the determination and documentation of chromosome numbers for extant taxa. This central cytological character has been used as an important phylogenetic marker and as an indicator for major genomic events such as polyploidy and dysploidy. Due to their significance and the relative ease by which chromosome numbers can be obtained, chromosome numbers have been extensively recorded across the plant kingdom and documented in a wide variety of resources. This makes the collection process a wearing task, often leading to partial data retrieval. In 2015, the Chromosome Counts Database (CCDB) was assembled, being an online unified community resource. This database compiles dozens of different chromosome counts sources, of which a significant portion had been unavailable before in a digitized, searchable format. The vast amount of data assembled in CCDB has already enabled a large number of analyses to examine the evolution of different plant hierarchies, as well as the application of various follow-up analyses, such as ploidy-level inference using chromEvol. CCDB ( http://ccdb.tau.ac.il/ ) encourages data sharing among the botanical community and is expected to continue expanding as additional chromosome numbers are recorded.

A pilot study for a non-invasive system for detection of malignancy in canine subcutaneous and cutaneous masses using machine learning.

Introduction: Early diagnosis of cancer enhances treatment planning and improves prognosis. Many masses presenting to veterinary clinics are difficult to diagnose without using invasive, time-consuming, and costly tests. Our objective was to perform a preliminary proof-of-concept for the HT Vista device, a novel artificial intelligence-based thermal imaging system, developed and designed to differentiate benign from malignant, cutaneous and subcutaneous masses in dogs. Methods: Forty-five dogs with a total of 69 masses were recruited. Each mass was clipped and heated by the HT Vista device. The heat emitted by the mass and its adjacent healthy tissue was automatically recorded using a built-in thermal camera. The thermal data from both areas were subsequently analyzed using an Artificial Intelligence algorithm. Cytology and/or biopsy results were later compared to the results obtained from the HT Vista system and used to train the algorithm. Validation was done using a "Leave One Out" cross-validation to determine the algorithm's performance. Results: The accuracy, sensitivity, specificity, positive predictive value, and negative predictive value of the system were 90%, 93%, 88%, 83%, and 95%, respectively for all masses. Conclusion: We propose that this novel system, with further development, could be used to provide a decision-support tool enabling clinicians to differentiate between benign lesions and those requiring additional diagnostics. Our study also provides a proof-of-concept for ongoing prospective trials for cancer diagnosis using advanced thermodynamics and machine learning procedures in companion dogs.

Inferring Chromosome Number Changes Along a Phylogeny Using chromEvol.

Chromosome numbers have long been used for the identification of key genomic events such as polyploidy and dysploidy. These inferences are often challenging, particularly when applied to large phylogenies, or clades in which more than a few chromosome number transitions had occurred. Here we describe the chromEvol computational framework that infers shifts in chromosome numbers along a phylogeny using probabilistic models of chromosome number change. Given chromosome count data and an associated phylogeny, chromEvol identifies such patterns by fitting probabilistic models of chromosome number evolution to the data. We describe the chromEvol workflow using available online tools, including the specification of the desired models, the examination of model fit to the data, and the inference of ploidy levels. The pipeline can be used by the wide scientific community and requires no previous computational or programming skills.

Interviews with parents of adolescents with intellectual and developmental disabilities in a weight management study.

BACKGROUND: Adolescents and young adults with intellectual and developmental disabilities are at risk of obesity. Parents influence their diet and physical activity behaviours and therefore, can play important roles in weight management. The aims of this qualitative study were to explore parents' experiences assisting their son or daughter to participate in a weight management study. METHODS: Interviews were completed at 6 months with 27 parents whose adolescent or young adult had completed the weight loss portion of an 18-month weight management study. Interviews were recorded, transcribed and thematic analysis performed. RESULTS: Parents shared insights about how well program components worked with their family, and what strategies worked best to adopt healthier dietary choices and become more physically active. The importance of meeting regularly with someone outside the family to encourage healthier habits was stressed. CONCLUSIONS: Future weight management studies should involve parents and their adolescents to help tailor strategies and adapt intervention approaches.

Androgen Deprivation and Sleep Disturbance: A Mixed Methods Pilot Study of Remote Assessment and Intervention.

BACKGROUND: Men receiving androgen deprivation therapy (ADT) for prostate cancer (PC) are at risk for cardiovascular comorbidities and cognitive changes. Interventional research involves in-person assessment of physical fitness/activity and cognitive function, which has been negatively affected by the COVID-19 pandemic. Androgen deprivation therapy-related hot flashes and nocturia increase risk for insomnia. Insomnia is associated with fatigue and may exacerbate ADT-related cognitive changes. OBJECTIVES: The purpose of this mixed-methods pilot was to (1) determine feasibility/acceptability of remotely assessing physical fitness/activity, cognitive function, and sleep; (2) deliver telehealth cognitive behavioral training for insomnia (teleCBT-I) to improve sleep; and (3) garner qualitative feedback to refine remote procedures and teleCBT-I content. METHODS: Fifteen men with PC receiving ADT completed a 4-week teleCBT-I intervention. Videoconferencing was used to complete study assessments and deliver the weekly teleCBT-I intervention. RESULTS: Self-report of sleep quality improved ( P < .001) as did hot flash frequency ( P = .04) and bother ( P = .025). Minimal clinically important differences were detected for changes in insomnia severity and sleep quality. All sleep logs indicated improvement in sleep efficiency. Remote assessment of fitness/cognitive function was demonstrated for 100% of participants. Sufficient actigraph wear time allowed physical activity/sleep assessment for 80%. Sleep actigraphy did not demonstrate significant changes. CONCLUSIONS: Remote monitoring and teleCBT-I are feasible/acceptable to men with PC on ADT. Further research to confirm teleCBT-I efficacy is warranted in this population. IMPLICATIONS FOR PRACTICE: Preliminary efficacy for teleCBT-I interventions was demonstrated. Remote assessments of physical fitness/activity, sleep, and cognitive function may enhance clinical trial access for rural or economically disadvantaged PC survivors.

A randomized trial comparing diet and delivery strategies for weight management in adolescents with intellectual disabilities.

BACKGROUND: The literature evaluating multi-component interventions for long-term weight loss in adolescents with intellectual disabilities (ID) is extremely limited. OBJECTIVES: To compare the effectiveness of two delivery strategies, face-to-face (FTF) or remote delivery (RD), and two diets, enhanced Stop Light diet (eSLD) or conventional diet (CD) on weight change across 12 and 18 months. in response to an 18 months. weight management intervention (6 months Weight loss/12 months. Weight maintenance) in adolescents with ID. METHODS: Adolescents with ID were randomized to one of three arms: FTF /CD, RD/CD, RD/eSLD and asked to attend individual education sessions with a health educator which were delivered during FTF home visits or remotely using video conferencing. The CD followed the US dietary guidelines. The eSLD utilized the Stop Light guide and was enhanced with portion-controlled meals. Participants were also asked to increase their physical activity (PA) and to self-monitor diet, PA and body weight across the 18-month. RESULTS: Weight was obtained from 92(84%) and 89(81%) randomized adolescents at 12 and 18 months, respectively. Weight change across 12 months. Differed significantly by diet (RD/eSLD: -7.0% vs. RD/CD: -1.1%, p = 0.002) but not by delivery strategy (FTF/CD: +1.1% vs. RD/CD: -1.1%, p = 0.21). Weight change across 18 months. Was minimal in all intervention arms and did not differ by diet (RD/eSLD: -2.6% vs. RD/CD: -0.5%; p = 0.28) or delivery strategy (FTF/CD: +1.6% vs. RD/CD: -0.5%; p = 0.47). CONCLUSIONS: Additional research is required to identify effective strategies to improve long-term weight loss in adolescents with ID.

Model adequacy tests for probabilistic models of chromosome-number evolution.

Chromosome number is a central feature of eukaryote genomes. Deciphering patterns of chromosome-number change along a phylogeny is central to the inference of whole genome duplications and ancestral chromosome numbers. ChromEvol is a probabilistic inference tool that allows the evaluation of several models of chromosome-number evolution and their fit to the data. However, fitting a model does not necessarily mean that the model describes the empirical data adequately. This vulnerability may lead to incorrect conclusions when model assumptions are not met by real data. Here, we present a model adequacy test for likelihood models of chromosome-number evolution. The procedure allows us to determine whether the model can generate data with similar characteristics as those found in the observed ones. We demonstrate that using inadequate models can lead to inflated errors in several inference tasks. Applying the developed method to 200 angiosperm genera, we find that in many of these, the best-fitting model provides poor fit to the data. The inadequacy rate increases in large clades or in those in which hybridizations are present. The developed model adequacy test can help researchers to identify phylogenies whose underlying evolutionary patterns deviate substantially from current modelling assumptions and should guide future methods development.

The global biogeography of polyploid plants.

Deciphering the global distribution of polyploid plants is fundamental for understanding plant evolution and ecology. Many factors have been hypothesized to affect the uneven distribution of polyploid plants across the globe. Nevertheless, the lack of large comparative datasets has restricted such studies to local floras and to narrow taxonomical scopes, limiting our understanding of the underlying drivers of polyploid plant distribution. We present a map portraying the worldwide polyploid frequencies, based on extensive spatial data coupled with phylogeny-based polyploidy inference for tens of thousands of species. This allowed us to assess the potential global drivers affecting polyploid distribution. Our data reveal a clear latitudinal trend, with polyploid frequency increasing away from the equator. Climate, especially temperature, appears to be the most influential predictor of polyploid distribution. However, we find this effect to be mostly indirect, mediated predominantly by variation in plant lifeforms and, to a lesser extent, by taxonomical composition and species richness. Thus, our study presents an emerging view of polyploid distribution that highlights attributes that facilitate the establishment of new polyploid lineages by providing polyploids with sufficient time (that is, perenniality) and space (low species richness) to compete with pre-adapted diploid relatives.

OneTwoTree: An online tool for phylogeny reconstruction.

Phylogeny reconstruction is a key instrument in numerous biological analyses, ranging from evolutionary and ecology research, to conservation and systems biology. The increasing accumulation of genomic data makes it possible to reconstruct phylogenies with both high accuracy and at increasingly finer resolution. Yet, taking advantage of the enormous amount of sequence data available requires the use of computational tools for efficient data retrieval and processing, or else the process could quickly become an error-prone endeavour. Here, we present OneTwoTree (http://onetwotree.tau.ac.il/), a Web-based tool for tree reconstruction based on the supermatrix paradigm. Given a list of taxa names of interest as the sole input requirement, OneTwoTree retrieves all available sequence data from NCBI GenBank, clusters these into orthology groups, identifies the most informative set of markers, searches for an appropriate outgroup, and assembles a partitioned sequence matrix that is then used for the final phylogeny reconstruction step. OneTwoTree further allows users to control various steps of the process, such as the merging of sequences from similar clusters, or phylogeny reconstruction based on markers from a specific genome type. By comparing the performance of OneTwoTree to a manually reconstructed phylogeny of the Antirrhineae tribe, we show that the use of OneTwoTree resulted in substantially higher data coverage in terms of both taxon sampling and the number of informative markers assembled. OneTwoTree provides a flexible online tool for species-tree reconstruction, aimed to assist researchers ranging in their level of prior expertise in the task of phylogeny reconstruction.

Detection of pregnancy-associated glycoproteins in milk and blood as a test for early pregnancy in dairy cows.

The objective of our study was to evaluate 2 pregnancy-associated glycoprotein (PAG)-based enzyme-linked immunosorbent assays (ELISAs) for use with either blood or milk. From 12 dairy farms, 116 Montbéliarde or Holstein cows were selected that had either undergone artificial insemination (AI; n = 102) or had calved (n = 14) 2-3 months earlier and had not undergone any further AI. Serum, plasma, and milk were obtained from all cows; serum and plasma were analyzed using the blood pregnancy test and milk using the milk pregnancy test. No false-positive results were observed when samples of the 14 noninseminated cows were tested. Cows undergoing AI were sampled at ~16, 30, and 41 days post-AI. An additional milk sample was taken at ~53 days post-AI. To establish whether the inseminated cows were pregnant, the cows were subjected to transrectal ultrasonography (TU) on or around day 41. Of the 102 inseminated cows, 63 were confirmed pregnant by TU. By day 30, the serum, plasma, and milk ELISAs demonstrated 100%, 100%, and 98.1% sensitivity and 88.6%, 88.9%, and 90.3% specificity, respectively, with potential pregnancy losses 30-41 days post-AI. Accuracy obtained on serum, plasma, and milk at ~41 days post-AI and on milk at ~53 days post-AI ranged from 97.4% to 100%. There were no differences of practical significance in performance between the blood and milk ELISAs for the sampling dates chosen. This new diagnostic capability with milk samples offers a major improvement in bovine reproductive management.

Kinetics of the porcine reproductive and respiratory syndrome virus (PRRSV) humoral immune response in swine serum and oral fluids collected from individual boars.

BACKGROUND: The object of this study was to describe and contrast the kinetics of the humoral response in serum and oral fluid specimens during acute porcine reproductive and respiratory syndrome virus (PRRSV) infection. The study involved three trials of 24 boars each. Boars were intramuscularly inoculated with a commercial modified live virus (MLV) vaccine (Trial 1), a Type 1 PRRSV field isolated (Trial 2), or a Type 2 PRRSV field isolate (Trial 3). Oral fluid samples were collected from individual boars on day post inoculation (DPI) -7 and 0 to 21. Serum samples were collected from all boars on DPI -7, 0, 7, 14, 21 and from 4 randomly selected boars on DPI 3, 5, 10, and 17. Thereafter, serum and oral fluid were assayed for PRRSV antibody using antibody isotype-specific ELISAs (IgM, IgA, IgG) adapted to serum or oral fluid. RESULTS: Statistically significant differences in viral replication and antibody responses were observed among the three trials in both serum and oral fluid specimens. PRRSV serum IgM, IgA, and IgG were first detected in samples collected on DPI 7, 10, and 10, respectively. Oral fluid IgM, IgA, and IgG were detected in samples collected between DPI 3 to 10, 7 to 10, and 8 to 14, respectively. CONCLUSIONS: This study enhanced our knowledge of the PRRSV humoral immune response and provided a broader foundation for the development and application of oral fluid antibody-based diagnostics.

Ring test evaluation of the repeatability and reproducibility of a Porcine reproductive and respiratory syndrome virus oral fluid antibody enzyme-linked immunosorbent assay.

The precision of a Porcine reproductive and respiratory syndrome virus (PRRSV) oral fluid antibody enzyme-linked immunosorbent assay (ELISA) was evaluated by calculating reliability coefficients for assay repeatability (within laboratory) and assay reproducibility (between laboratories). Randomly ordered oral fluid samples of known (n = 39) and unknown (n = 224) PRRSV antibody status were tested in 12 diagnostic laboratories. Each laboratory tested the samples twice, first using an antibody ELISA kit and reagents provided to them (phase 1) and then using an ELISA kit and reagents configured in their respective laboratory (phase 2). Repeatability (within laboratory) reliability coefficients calculated using results from samples of known PRRSV antibody status ranged from 0.724 to 0.997 in phase 1 and from 0.953 to 0.998 in phase 2. Reproducibility (between laboratories) reliability coefficients were calculated for 3 conditions: case 1--samples of unknown status (n = 224); case 2--samples of known status (n = 39), and case 3--all samples (n = 263). Among the 3 cases, reliability coefficients ranged from 0.937 to 0.964 in phase 1 and from 0.922 to 0.935 in phase 2. For case 3, it was estimated that 96.67% of the total variation in phase 1 and 93.21% in phase 2 could be attributed to the oral fluid samples themselves. Overall, the PRRSV oral fluid antibody ELISA was highly repeatable and reproducible. The current study supports the routine use of this test in laboratories providing diagnostic service to pig producers.

Detection of Porcine reproductive and respiratory syndrome virus (PRRSV) antibodies in oral fluid specimens using a commercial PRRSV serum antibody enzyme-linked immunosorbent assay.

The purpose of the present study was to evaluate the diagnostic performance of a commercial serum antibody enzyme-linked immunosorbent assay (ELISA) modified to detect anti-Porcine reproductive and respiratory syndrome virus (PRRSV) antibodies in pen-based oral fluid specimens. Experimental and field oral fluid samples of defined status in reference to exposure of swine with PRRSV were used to derive the kinetics of detectable concentrations of antibody against PRRSV. Immunoglobulin (Ig)M and IgA were readily detected in oral fluid specimens from populations in which PRRSV infection was synchronized among all individuals but not in samples collected in commecial herds. In contrast, IgG was readily detected at diagnostically useful levels in both experimental and field samples for up to 126 days. Estimates of the IgG oral fluid ELISA performance were based on results from testing positive oral fluid samples (n = 492) from experimentally inoculated pigs (n = 251) and field samples (n = 241) and negative oral fluid samples (n = 367) from experimentally inoculated pigs (n = 84) and field samples (n = 283). Receiver operating characteristic analysis estimated the diagnostic sensitivity and specificity of the assay as 94.7% (95% confidence interval [CI]: 92.4, 96.5) and 100% (95% CI: 99.0, 100.0), respectively, at a sample-to-positive ratio cutoff of ≥0.40. The results of the study suggest that the IgG oral fluid ELISA can provide efficient, cost-effective PRRSV monitoring in commercial herds and PRRSV surveillance in elimination programs.

Inhibition of all-trans retinoic acid-induced granulocytic differentiation of WEHI-3B D+ cells by forced expression of SCL (TAL1) and GATA-1.

All-trans retinoic acid (ATRA) induces granulocytic maturation of WEHI-3B D+ leukemia cells and LiCl enhances this maturation, while WEHI-3B D- cells are non-responsive to ATRA. Transfection of SCL, expressed in D- but absent in D+ cells, into D+ cells, caused resistance to ATRA, while transfection of GATA-1 into D+ cells produced resistance to the combination of ATRA and LiCl. SCL expression in D+ cells did not induce the expression of c-Kit, a putative target gene for SCL. LiCl, known to inhibit some kinases by displacing Mg2+, did not affect tyrosine kinase activity of the cytoplasmic domain of c-Kit.

Increasing customer service behaviors using manager-delivered task clarification and social praise.

This project assessed an intervention to improve employee customer service behaviors (correct greetings and closing behaviors). A combination of task clarification and manager-delivered social praise resulted in increased correct greeting from 11.5% to 66% and correct closing from 8% to 70%. The effect was maintained at a 48-week follow-up for employees who were present during the initial study period, but not for more recently hired employees. The results suggest that task clarification combined with manager-delivered social praise is an effective way to improve employee customer service behaviors.

Oncoprotein EWS-FLI1 activity is enhanced by RNA helicase A.

RNA helicase A (RHA), a member of the DEXH box helicase family of proteins, is an integral component of protein complexes that regulate transcription and splicing. The EWS-FLI1 oncoprotein is expressed as a result of the chromosomal translocation t(11;22) that occurs in patients with the Ewing's sarcoma family of tumors (ESFT). Using phage display library screening, we identified an EWS-FLI1 binding peptide containing homology to RHA. ESFT cell lines and patient tumors highly expressed RHA. GST pull-down and ELISA assays showed that EWS-FLI1 specifically bound RHA fragment amino acids 630 to 1020, which contains the peptide region discovered by phage display. Endogenous RHA was identified in a protein complex with EWS-FLI1 in ESFT cell lines. Chromatin immunoprecipitation experiments showed both EWS-FLI1 and RHA bound to EWS-FLI1 target gene promoters. RHA stimulated the transcriptional activity of EWS-FLI1 regulated promoters, including Id2, in ESFT cells. In addition, RHA expression in mouse embryonic fibroblast cells stably transfected with EWS-FLI1 enhanced the anchorage-independent phenotype above that with EWS-FLI1 alone. These results suggest that RHA interacts with EWS-FLI1 as a transcriptional cofactor to enhance its function.

Analysis of the relationship between Scl transcription factor complex protein expression patterns and the effects of LiCl on ATRA-induced differentiation in blast cells from patients with acute myeloid leukemia.

Exogenous expression of the transcription factor Scl (Tal1) in WEHI-3B D+ myelomonocytic leukemia cells interferes with their capacity to respond to all-trans retinoic acid (ATRA) induced differentiation; combination of ATRA with LiCl, however, circumvents the inhibition of differentiation produced by Scl. To gain information on the possible involvement of this transcription factor in the non-responsiveness of acute myelocytic leukemia (AML) patients to ATRA, we compared the endogenous expression levels of Scl and its transcription complex partners [i.e., Rbtn1 (LMO1), Rbtn2 (LMO2), Ldb1, and GATA family proteins] in leukemic blast cells from patients with AML and acute promyelocytic leukemia (APL), and determined the effects of lithium chloride alone or in combination with ATRA on the capacity of blast cells to differentiate during short-term ex vivo culture. Levels of Scl, Rbtn2, GATA1, and Ldb1 expression were comparable in AML and APL blasts, while the levels of expression of Rbtn1, GATA2, and GATA3 were absent or markedly lower in APL cells. Differentiation markers (cell surface myeloid antigens CD11b, CD15, CD14, and CD33) were also analyzed in blast cells. ATRA produced changes in at least one surface antigen differentiation marker in 89% of patient blasts, while LiCl caused such changes in 72% of the leukemic cells of patients. The combination of LiCl and ATRA induced the differentiation of leukemic blasts from 94% of patients. Although the expression of the transcription factors did not act as individual predictors of responsiveness or non-responsiveness to the inducers of differentiation, ATRA or ATRA plus LiCl, the addition of LiCl to ATRA increased the differentiation response over that of ATRA alone in a number of leukemic samples. These findings suggest that the combination of LiCl and ATRA may produce some clinical benefit in the treatment of the myeloid leukemias.

Combination of all-trans retinoic acid and lithium chloride surmounts a retinoid differentiation block induced by expression of Scl and Rbtn2 transcription factors in myeloid leukemia cells.

We have previously shown that forced expression of the transcription factor Scl in WEHI-3B D(+) cells prevents ATRA-induced cell differentiation. We now find that the overexpression of Rbtn2 also interferes with induction of differentiation by ATRA. Addition of LiCl to ATRA treatment restored the capacity of both Scl- and Rbtn2-expressing cells to respond to the retinoid in a synergistic manner. Similar results were obtained with Scl-transfected HL60 cells where its expression diminished responsiveness to ATRA. These findings suggest that if Scl and/or Rbtn2 are involved in the non-responsiveness of AML patients to ATRA-induced differentiation, addition of LiCl may reverse insensitivity.