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Rujuta Saksena, Serena T WongThe Cancer Institute of New Jersey, New Brunswick, NJ, USAAbstract: The PI3K/Akt/mTOR (phosphatidylinositol 3-kinase/protein kinase B/mammalian target of rapamycin) pathway regulates several key cellular functions and its dysregulation creates an environment that promotes tumorigenesis as well as resistance to therapy. The mTOR inhibitor everolimus has emerged as a promising agent in the treatment of breast cancer and was recently approved in combination with exemestane for advanced hormone receptor–positive disease after progression on a nonsteroidal aromatase inhibitor. Everolimus may also be effective in combination with cytotoxic and human epidermal growth factor receptor-2-directed therapies for the treatment of other subtypes of breast cancer. This paper highlights preclinical and clinical data that have emerged on the role of mTOR inhibition in breast cancer. Although generally well tolerated, everolimus carries a unique side effect profile of which both patients and providers should be made aware. Recommendations related to the administration of everolimus in the clinical setting are also discussed.Keywords: everolimus, breast cancer, mTOR inhibition

Alzheimer’s disease and related dementias (AD/ADRD) affects more than 50 million people worldwide but there is no clear therapeutic option affordable for the general patient population. Recently, drug repositioning studies featuring collaborations between academic institutes, medical centers, and hospitals are generating novel therapeutics candidates against these devastating diseases and filling in an important area for healthcare that is poorly represented by pharmaceutical companies. Such drug repositioning studies converge expertise from bioinformatics, chemical informatics, medical informatics, artificial intelligence, high throughput and high-content screening and systems biology. They also take advantage of multi-scale, multi-modality datasets, ranging from transcriptomic and proteomic data, electronical medical records, and medical imaging to social media information of patient behaviors and emotions and epidemiology profiles of disease populations, in order to gain comprehensive understanding of disease mechanisms and drug effects. We proposed a recursive drug repositioning paradigm involving the iteration of three processing steps of modeling, prediction, and validation to identify known drugs and bioactive compounds for AD/ADRD. This recursive paradigm has the potential of quickly obtaining a panel of robust novel drug candidates for AD/ADRD and gaining in-depth understanding of disease mechanisms from those repositioned drug candidates, subsequently improving the success rate of predicting novel hits.

Objective. To study the effects of the three methods and three-acupoint technique on DRG gene expression in SNI model rats and to elucidate the molecular mechanism of the three methods and three-acupoint technique on promoting recovery in peripheral nerve injury. Methods. 27 male SD rats were randomly divided into three groups: a Sham group, the SNI group, and the Tuina group. The Tuina group was treated with a tuina manipulation simulator to simulate massage on points, controlling for both quality and quantity. Point-pressing, plucking, and kneading methods were administered quantitatively at Yinmen (BL37), Chengshan (BL57), and Yanglingquan (GB34) points on the affected side once a day, beginning 7 days after modeling. Intervention was applied once a day for 10 days, then 1 day of rest, followed by 10 more days of intervention, totally equaling 20 times of intervention. The effect of the three methods and three-point technique on the recovery of injured rats was evaluated using behavior analysis. RNA sequencing (RNA-Seq) analysis of differentially expressed genes in DRGs of the three groups of rats was also performed. GO and KEGG enrichment was analyzed and verified using real-time PCR. Results. RNA-Seq combined with database information showed that the number of differentially expressed genes in DRG was the largest in the Tuina group compared with the SNI group, totaling 226. GO function is enriched in the positive regulation of cell processes, ion binding, protein binding, neuron, response to pressure, response to metal ions, neuron projection, and other biological processes. GO function is also enriched in the Wnt, IL-17, and MAPK signaling pathways in the KEGG database. PCR results were consistent with those of RNA sequencing, suggesting that the results of transcriptome sequencing were reliable. Conclusion. The three methods and three-acupoint technique can promote the recovery of SNI model rats by altering the gene sequence in DRGs.

Rationale and Objectives: Quantitative measurement provides essential information about disease progression and treatment response in patients with glioblastoma multiforme (GBM). The goal of this article is to present and validate a software pipeline for semi-automatic GBM segmentation, called AFINITI (Assisted Follow-up in NeuroImaging of Therapeutic Intervention), using clinical data from GBM patients.Materials and Methods: Our software adopts the current state-of-the-art tumor segmentation algorithms and combines them into one clinically usable pipeline. Both the advantages of the traditional voxel-based and the deformable shape-based segmentation are embedded into the software pipeline. The former provides an automatic tumor segmentation scheme based on T1- and T2-weighted magnetic resonance (MR) brain data, and the latter refines the segmentation results with minimal manual input.Results: Twenty-six clinical MR brain images of GBM patients were processed and compared with manual results. The results can be visualized using the embedded graphic user interface.Conclusion: Validation results using clinical GBM data showed high correlation between the AFINITI results and manual annotation. Compared to the voxel-wise segmentation, AFINITI yielded more accurate results in segmenting the enhanced GBM from multimodality MR imaging data. The proposed pipeline could be used as additional information to interpret MR brain images in neuroradiology. [ABSTRACT FROM AUTHOR]

Objective: This study examined ethnic disparities in antipsychotic therapy in a population with significant Asian representation.Methods: Using a cross-sectional retrospective study design, self-reported ethnicity data pooled from three cycles of the Canadian Community Health Survey were linked to 2005 administrative data on physician, hospital, and pharmaceutical use in British Columbia, Canada. Logistic regression was used to model the association between ethnicity and the likelihood of filling one or more prescriptions for any antipsychotic, with controls for sex, age, residence, immigrant status, income, health status, and diagnoses of schizophrenia, bipolar disorder, depression, and dementia.Results: Of the 27,658 individuals in the sample, 2.2% filled at least one antipsychotic prescription. The proportion varied across ethnic groups: Chinese, 1.0%; other Asians, 1.2%; whites, 2.3%; nonwhite non-Asians, 2.8%; and mixed ethnicity, 4.3%. After adjustment for patient characteristics and diagnoses of schizophrenia and bipolar disorder, the likelihood of filling a prescription was found to be lower among Chinese (odds ratio [OR] = .47, 95% confidence interval [CI] = .24-.90) and higher among persons of mixed ethnicity (OR = 3.19, CI = 1.49-6.83). Further adjustment for depression and dementia diagnoses did not significantly change the ORs for the Chinese (OR = .49, CI = .25-.98) and the mixed ethnic groups (OR = 2.97, CI = 1.30-6.80).Conclusions: Consistent with the existing literature on ethnic disparities in antipsychotic therapy, the study found evidence of persistent disparities in a population that has a significant number of Asians. Further studies should be done to identify possible causes of these disparities and to identify potential interventions that may reduce or eliminate them. [ABSTRACT FROM AUTHOR]

The Cadi ThermoSENSOR skin-contact thermometer measures body temperature continuously and transmits readings wirelessly to a central server. This study evaluated the ThermoSENSOR against ear temperatures (ETs) measured by a Braun ThermoScan ear thermometer and axillary temperatures (ATs) measured by a Terumo digital clinical thermometer. The test participants consisted of 109 children aged 6 months to 16 years from a pediatric ward. The sensor was attached to the lower abdomen at least 15 minutes before the first measurement. ET, AT, and ThermoSENSOR temperatures (TTs) were recorded up to three times at the usual measurement times. The TTs differed from ETs by -0.23 degrees C +/- 0.47 degrees C (mean +/- standard deviation, n = 271) and from ATs by +0.21 degrees C +/- 0.46 degrees C (n = 270). The ETs differed from ATs by +0.43 degrees C +/- 0.42 degrees C (n = 315). These results suggest that the TTs were comparable to the ETs and ATs.Copyright © 2010 by Elsevier Inc. [ABSTRACT FROM AUTHOR]

One result of the widespread screening mammography is a 200% increase in the rates of breast ductal carcinoma in situ (DCIS). Treatment decision making among Chinese women diagnosed with DCIS remains understudied. This study examined Chinese-Canadian women's experiences (N = 26): (1) with treatment decision making (mastectomy or breast conserving surgery) and (2) their reflections on the decision-making process. Interviews in Cantonese, Mandarin, or English were transcribed and translated, and a content analysis conducted. Women's treatment decisions reflected a lack of understanding of DCIS, the desire to rid themselves of breast cancer forever, and the influence of significant others. English as a second language and use of medical jargon impeded their ability to make informed treatment decisions. Women's reflections on the decision-making process provided insights into how to improve information and support treatment decision making in ways that are accessible to them. [ABSTRACT FROM AUTHOR]

This study explored social support domains and actual sources of support for older Chinese and Korean immigrants and compared them to the traditional domains based on mainly White, middle class populations. Fifty-two older Cantonese and Korean speaking immigrants participated in one of eight focus groups. We identified four similar domains: tangible, information/advice, emotional support, and companionship. We also identified needing language support which is relevant for non-English speaking minority populations. Participants discussed not needing emotional support. These Chinese and Korean immigrants had a small number of actual sources of support, relying mainly on adult children for help with personal situations (e.g., carrying heavy groceries, communicating with physicians) and friends for general information/advice (e.g., learning how to speak English, applying for citizenship) and companionship. Immigrant Asians are caught between two different traditions; one that is strongly kinship oriented where needs and desires are subordinated to the interests of the family and one that values independence and celebrates individuality. Despite their reticence in asking for help outside the family, elders are seeking help from other sources, such as ethnic churches and the government. [ABSTRACT FROM AUTHOR]

OBJECTIVES: If prenatal health promotion and psychosocial support services are to remain accessible to Medicaid eligible women, evidence is needed as to whether the services improve care and benefit women in ways that matter to health plans. The aims of this study are to determine whether prenatal health promotion and psychosocial services are associated with better interpersonal care and greater satisfaction with care; and whether the effects on interpersonal care help explain satisfaction with care. RESEARCH DESIGN: A telephone survey of 363 African American, Latina (US and nonUS-born) and White women receiving prenatal care in four Medicaid public health plans in California in 2001. Multivariate regression analyses were done with adjustments for potentially confounding variables. MEASURES: Independent variables included dichotomous variables for health promotion advice (five separate areas) and composite scales for psychosocial assessment (six areas combined). Dependent variables included satisfaction with care, and indices for interpersonal care (communication, decision-making, and interpersonal style). RESULTS: Women who report receiving health promotion or psychosocial services also report receiving better interpersonal care and rate their satisfaction with care higher. Receiving either type of support service is associated with higher quality communication, decision-making and interpersonal style. The effects of the support services on satisfaction are, in turn, explained by the effects on interpersonal care. CONCLUSIONS: Prenatal health promotion and psychosocial services have associated benefits to enrollees that should matter to Medicaid health plans and their providers. [ABSTRACT FROM AUTHOR]

PURPOSE: To examine health care spending patterns for U.S. adolescents aged 10 to 18 years using nationally representative household survey data. METHODS: We analyzed data from the 1997 Medical Expenditure Panel Survey on total expenditures and out-of-pocket expenditures for health care based on a sample of 4882 adolescents. RESULTS: Compared with that for adults, health care expenditures for adolescents were low, averaging $799 US dollars per adolescent in 1997. Disabled and functionally impaired adolescents had disproportionately high expenditures ($1960 US dollars per capita). Blacks and adolescents living in poor families had disproportionately low expenditures ($358 and $609 US dollars per capita, respectively). Professional services provided by physicians and dentists accounted for more than one-half of all health care spending for adolescents. Only 2% of adolescents were hospitalized in 1997, but they accounted for about one-fifth of all health care expenditures. The share of health expenditures paid out of pocket varied by type of service, ranging from 3% for inpatient hospital care to 51% for dental care. When covered, insurance provided substantial financial protection for families of adolescents: those with public coverage paid 8%, those with private coverage paid 32%, and those without coverage paid 61% of their health care bills out of pocket. The share of health care bills paid out of pocket would be much lower if dental care was excluded. CONCLUSIONS: On the basis of our findings that health care expenditures for adolescents are low and that insurance coverage provides critically needed financial protection, we conclude that further expansions of public and private health insurance coverage for this population would provide significant benefits at modest additional cost. Additional efforts to improve coverage of services that are not now well-covered, such as dental care, would also be valuable. [ABSTRACT FROM AUTHOR]

Tuina is a traditional Chinese treatment for sensory disturbances caused by peripheral nerve injury and related diseases. Our previous studies showed that tuina regulates relevant regions and indices of the spinal dorsal horn using the Dian, Bo, and Rou method in Yinmen (BL37), Yanglingquan (GB34), and Weizhong (BL40). Treatment prevents muscle atrophy, protects spinal cord neurons, and promotes sciatic nerve repair. The mechanisms of action of tuina for treating peripheral nerve injury remain poorly understood. This study established rat models of sciatic nerve injury using the crushing method. Rats received Chinese tuina in accordance with the principle of “Three Methods and Three Points,” once daily for 20 days. Tuina intervention reduced paw withdrawal latency and improved wet weight of the gastrocnemius muscle, as well as promoting morphological recovery of sciatic nerve fibers, Schwann cells, and axons. The protein expression levels of phospho-p38 mitogen-activated protein kinase, tumor necrosis factor-α, and interleukin-1β also decreased. These findings indicate that “Three Methods and Three Points” promoted morphological recovery and improved behavior of rats with peripheral nerve injury.

Abstract Background Detection of mutations by DNA sequencing can be facilitated by scanning methods to identify amplicons which may have mutations. Current scanning methods used for the detection of germline sequence variants are laborious as they require post-PCR manipulation. High resolution melting (HRM) is a cost-effective rapid screening strategy, which readily detects heterozygous variants by melting curve analysis of PCR products. It is well suited to screening genes such as BRCA1 and BRCA2 as germline pathogenic mutations in these genes are always heterozygous. Methods Assays for the analysis of all coding regions and intron-exon boundaries of BRCA1 and BRCA2 were designed, and optimised. A final set of 94 assays which ran under identical amplification conditions were chosen for BRCA1 (36) and BRCA2 (58). Significant attention was placed on primer design to enable reproducible detection of mutations within the amplicon while minimising unnecessary detection of polymorphisms. Deoxyinosine residues were incorporated into primers that overlay intronic polymorphisms. Multiple 384 well plates were used to facilitate high throughput. Results 169 BRCA1 and 239 BRCA2 known sequence variants were used to test the amplicons. We also performed an extensive blinded validation of the protocol with 384 separate patient DNAs. All heterozygous variants were detected with the optimised assays. Conclusions This is the first HRM approach to screen the entire coding region of the BRCA1 and BRCA2 genes using one set of reaction conditions in a multi plate 384 well format using specifically designed primers. The parallel screening of a relatively large number of samples enables better detection of sequence variants. HRM has the advantages of decreasing the necessary sequencing by more than 90%. This markedly reduced cost of sequencing will result in BRCA1 and BRCA2 mutation testing becoming accessible to individuals who currently do not undergo mutation testing because of the significant costs involved.

Abstract Background Insufficient participation in physical activity and excessive screen time have been observed among Chinese children. The role of social and environmental factors in shaping physical activity and sedentary behaviors among Chinese children is under-investigated. The purpose of the present study was to assess the reliability and validity of a questionnaire to measure child- and parent-reported psychosocial and environmental correlates of physical activity and screen-based behaviors among Chinese children in Hong Kong. Methods A total of 303 schoolchildren aged 9-14 years and their parents volunteered to participate in this study and 160 of them completed the questionnaire twice within an interval of 10 days. Intraclass correlation coefficients (ICCs), kappa statistics, and percent agreement were performed to evaluate test-retest reliability of the continuous and categorical variables, respectively. Exploratory factor analyses (EFAs) were conducted to assess convergent validity of the emergent scales. Cronbach's alpha and ICCs were performed to assess internal and test-retest reliability of the emergent scales. Criterion validity was assessed by correlating psychosocial and environmental measures with self-reported physical activity and screen-based behaviors, measured by a validated questionnaire. Results Reliability statistics for both child- and parent-reported continuous variables showed acceptable consistency for all of the ICC values greater than 0.70. Kappa statistics showed fair to perfect test-retest reliability for the categorical items. Adequate internal consistency and test-retest reliability were observed in most of the emergent scales. Criterion validity assessed by correlating psychosocial and environmental measures with child-reported physical activity found associations with physical activity in the self-efficacy scale (r = 0.25, P < 0.05), the peer support for physical activity scale (r = 0.25, P < 0.05) and home physical activity environmental (r = 0.14, P < 0.05). Children's screen-based behaviors were associated with the family support for physical activity scale (r = -0.22, P < 0.05) and parental role modeling of TV (r = 0.12, P = 0.053). Conclusions The findings provide psychometric support for using this questionnaire for examining psychosocial and environmental correlates of physical activity and screen-based behaviors among Chinese children in Hong Kong. Further research is needed to develop more robust measures based on the current questionnaire, especially for peer influence on physical activity and parental rules on screen-based behaviors.

Abstract Background DNA copy number aberration (CNA) is very important in the pathogenesis of tumors and other diseases. For example, CNAs may result in suppression of anti-oncogenes and activation of oncogenes, which would cause certain types of cancers. High density single nucleotide polymorphism (SNP) array data is widely used for the CNA detection. However, it is nontrivial to detect the CNA automatically because the signals obtained from high density SNP arrays often have low signal-to-noise ratio (SNR), which might be caused by whole genome amplification, mixtures of normal and tumor cells, experimental noise or other technical limitations. With the reduction in SNR, many false CNA regions are often detected and the true CNA regions are missed. Thus, more sophisticated statistical models are needed to make the CNAs detection, using the low SNR signals, more robust and reliable. Results This paper presents a conditional random pattern (CRP) model for CNA detection where much contextual cues are explored to suppress the noise and improve CNA detection accuracy. Both simulated and the real data are used to evaluate the proposed model, and the validation results show that the CRP model is more robust and reliable in the presence of noise for CNA detection using high density SNP array data, compared to a number of widely used software packages. Conclusions The proposed conditional random pattern (CRP) model could effectively detect the CNA regions in the presence of noise.

Abstract Background Several γ-secretase inhibitors (GSI) are in clinical trials for the treatment of Alzheimer's disease (AD). This enzyme mediates the proteolytic cleavage of amyloid precursor protein (APP) to generate amyloid β protein, Aβ, the pathogenic protein in AD. The γ-secretase also cleaves Notch to generate Notch Intracellular domain (NICD), the signaling molecule that is implicated in tumorigenesis. Results We have developed a method to examine live zebrafish that were each treated with γ-secretase inhibitors (GSI), DAPT {N- [N-(3,5-Difluorophenacetyl-L-alanyl)]-S-phenylglycine t-Butyl Ester}, Gleevec, or fragments of Gleevec. These compounds were first tested in a cell-based assay and the effective concentrations of these compounds that blocked Aβ generation were quantitated. The mortality of zebrafish, as a result of exposure to different doses of compound, was assessed, and any apoptotic processes were examined by TUNEL staining. We then used conventional and automatic microscopes to acquire images of zebrafish and applied algorithms to automate image composition and processing. Zebrafish were treated in 96- or 384-well plates, and the phenotypes were analyzed at 2, 3 and 5 days post fertilization (dpf). We identified that AD95, a fragment of Gleevec, effectively blocks Aβ production and causes specific phenotypes that were different from those treated with DAPT. Finally, we validated the specificity of two Notch phenotypes (pigmentation and the curvature of tail/trunk) induced by DAPT in a dose-dependent manner. These phenotypes were examined in embryos treated with GSIs or AD95 at increasing concentrations. The expression levels of Notch target gene her6 were also measured by in situ hybridization and the co-relationship between the levels of Notch inhibition by DAPT and AD95 and the severity of phenotypes were determined. Conclusion The results reported here of the effects on zebrafish suggest that this newly developed method may be used to screen novel GSIs and other leads for a variety of therapeutic indications.

Abstract Background Cancer and Alzheimer's disease (AD) are two seemingly distinct diseases and rarely occur simultaneously in patients. To explore molecular determinants differentiating pathogenic routes towards AD or cancer, we investigate the role of amyloid β protein (Aβ) on multiple tumor cell lines that are stably expressing luciferase (human glioblastoma U87; human breast adenocarcinoma MDA-MB231; and mouse melanoma B16F). Results Quantification of the photons emitted from the MDA-MB231 or B16F cells revealed a significant inhibition of cell proliferation by the conditioning media (CM) derived from amyloid precursor protein (APP) over-expressing cells. The inhibition of U87 cells was observed only after the media was conditioned for longer than 2 days with APP over-expressing cells. Conclusion Our results suggest that Aβ plays an inhibitory role in tumor cell proliferation; this effect could depend on the type of tumor cells and amount of Aβ.

Abstract Identification of neutralizing antibodies with specificity away from the traditional mutation prone antigenic regions, against the conserved regions of hemagglutinin from H5N1 influenza virus has the potential to provide a therapeutic option which can be developed ahead of time in preparation for a possible pandemic due to H5N1 viruses. In this study, we used a combination of panning strategies against the hemagglutinin (HA) of several antigenic distinct H5N1 isolates to bias selection of Fab-phage from a naïve human library away from the antigenic regions of HA, toward the more conserved portions of the protein. All of the identified Fab clones which showed binding to multiple antigenically distinct HA were converted to fully human IgG, and tested for their ability to neutralize the uptake of H5N1-virus like particles (VLP) into MDCK cells. Five of the antibodies which showed binding to the relatively conserved HA2 subunit of HA, exhibited neutralization of H5N1-VLP uptake in a dose dependant manner. The inhibitory effects of these five antibodies were similar to those observed with a previously described neutralizing antibody specific for the 140s antigenic loop present within HA1 and highlight the exciting possibility that these antibodies may be efficacious against multiple H5N1 strains.

Abstract The monoclonal antibody VN04-2 was previously shown to protect mice against lethal A/Vietnam/1203/04 H5N1 virus challenge when administered pre- and post-infection. In this study, we characterized the binding requirements of this antibody using direct binding to hemagglutinin and neutralization assays with H5N1 virus-like particles (H5N1-VLP) of eight recent H5N1 strains representing the major mutations within the 140s antigenic loop. Binding was clade independent and 3 mutations within this antigenic region are required before escape is possible, suggesting that apart from the H5N1 viruses circulating in Indonesia, VN04-2 may provide protection against H5N1 viruses from all other regions.

Abstract Background The recent emergence of high-throughput automated image acquisition technologies has forever changed how cell biologists collect and analyze data. Historically, the interpretation of cellular phenotypes in different experimental conditions has been dependent upon the expert opinions of well-trained biologists. Such qualitative analysis is particularly effective in detecting subtle, but important, deviations in phenotypes. However, while the rapid and continuing development of automated microscope-based technologies now facilitates the acquisition of trillions of cells in thousands of diverse experimental conditions, such as in the context of RNA interference (RNAi) or small-molecule screens, the massive size of these datasets precludes human analysis. Thus, the development of automated methods which aim to identify novel and biological relevant phenotypes online is one of the major challenges in high-throughput image-based screening. Ideally, phenotype discovery methods should be designed to utilize prior/existing information and tackle three challenging tasks, i.e. restoring pre-defined biological meaningful phenotypes, differentiating novel phenotypes from known ones and clarifying novel phenotypes from each other. Arbitrarily extracted information causes biased analysis, while combining the complete existing datasets with each new image is intractable in high-throughput screens. Results Here we present the design and implementation of a novel and robust online phenotype discovery method with broad applicability that can be used in diverse experimental contexts, especially high-throughput RNAi screens. This method features phenotype modelling and iterative cluster merging using improved gap statistics. A Gaussian Mixture Model (GMM) is employed to estimate the distribution of each existing phenotype, and then used as reference distribution in gap statistics. This method is broadly applicable to a number of different types of image-based datasets derived from a wide spectrum of experimental conditions and is suitable to adaptively process new images which are continuously added to existing datasets. Validations were carried out on different dataset, including published RNAi screening using Drosophila embryos [Additional files 1, 2], dataset for cell cycle phase identification using HeLa cells [Additional files 1, 3, 4] and synthetic dataset using polygons, our methods tackled three aforementioned tasks effectively with an accuracy range of 85%–90%. When our method is implemented in the context of a Drosophila genome-scale RNAi image-based screening of cultured cells aimed to identifying the contribution of individual genes towards the regulation of cell-shape, it efficiently discovers meaningful new phenotypes and provides novel biological insight. We also propose a two-step procedure to modify the novelty detection method based on one-class SVM, so that it can be used to online phenotype discovery. In different conditions, we compared the SVM based method with our method using various datasets and our methods consistently outperformed SVM based method in at least two of three tasks by 2% to 5%. These results demonstrate that our methods can be used to better identify novel phenotypes in image-based datasets from a wide range of conditions and organisms. Conclusion We demonstrate that our method can detect various novel phenotypes effectively in complex datasets. Experiment results also validate that our method performs consistently under different order of image input, variation of starting conditions including the number and composition of existing phenotypes, and dataset from different screens. In our findings, the proposed method is suitable for online phenotype discovery in diverse high-throughput image-based genetic and chemical screens.

Abstract Background High content screening (HCS)-based image analysis is becoming an important and widely used research tool. Capitalizing this technology, ample cellular information can be extracted from the high content cellular images. In this study, an automated, reliable and quantitative cellular image analysis system developed in house has been employed to quantify the toxic responses of human H4 neuroglioma cells exposed to metal oxide nanoparticles. This system has been proved to be an essential tool in our study. Results The cellular images of H4 neuroglioma cells exposed to different concentrations of CuO nanoparticles were sampled using IN Cell Analyzer 1000. A fully automated cellular image analysis system has been developed to perform the image analysis for cell viability. A multiple adaptive thresholding method was used to classify the pixels of the nuclei image into three classes: bright nuclei, dark nuclei, and background. During the development of our image analysis methodology, we have achieved the followings: (1) The Gaussian filtering with proper scale has been applied to the cellular images for generation of a local intensity maximum inside each nucleus; (2) a novel local intensity maxima detection method based on the gradient vector field has been established; and (3) a statistical model based splitting method was proposed to overcome the under segmentation problem. Computational results indicate that 95.9% nuclei can be detected and segmented correctly by the proposed image analysis system. Conclusion The proposed automated image analysis system can effectively segment the images of human H4 neuroglioma cells exposed to CuO nanoparticles. The computational results confirmed our biological finding that human H4 neuroglioma cells had a dose-dependent toxic response to the insult of CuO nanoparticles.

Abstract Background Reliable segmentation of cell nuclei from three dimensional (3D) microscopic images is an important task in many biological studies. We present a novel, fully automated method for the segmentation of cell nuclei from 3D microscopic images. It was designed specifically to segment nuclei in images where the nuclei are closely juxtaposed or touching each other. The segmentation approach has three stages: 1) a gradient diffusion procedure, 2) gradient flow tracking and grouping, and 3) local adaptive thresholding. Results Both qualitative and quantitative results on synthesized and original 3D images are provided to demonstrate the performance and generality of the proposed method. Both the over-segmentation and under-segmentation percentages of the proposed method are around 5%. The volume overlap, compared to expert manual segmentation, is consistently over 90%. Conclusion The proposed algorithm is able to segment closely juxtaposed or touching cell nuclei obtained from 3D microscopy imaging with reasonable accuracy.

Abstract Background Automated identification of cell cycle phases of individual live cells in a large population captured via automated fluorescence microscopy technique is important for cancer drug discovery and cell cycle studies. Time-lapse fluorescence microscopy images provide an important method to study the cell cycle process under different conditions of perturbation. Existing methods are limited in dealing with such time-lapse data sets while manual analysis is not feasible. This paper presents statistical data analysis and statistical pattern recognition to perform this task. Results The data is generated from Hela H2B GFP cells imaged during a 2-day period with images acquired 15 minutes apart using an automated time-lapse fluorescence microscopy. The patterns are described with four kinds of features, including twelve general features, Haralick texture features, Zernike moment features, and wavelet features. To generate a new set of features with more discriminate power, the commonly used feature reduction techniques are used, which include Principle Component Analysis (PCA), Linear Discriminant Analysis (LDA), Maximum Margin Criterion (MMC), Stepwise Discriminate Analysis based Feature Selection (SDAFS), and Genetic Algorithm based Feature Selection (GAFS). Then, we propose a Context Based Mixture Model (CBMM) for dealing with the time-series cell sequence information and compare it to other traditional classifiers: Support Vector Machine (SVM), Neural Network (NN), and K-Nearest Neighbor (KNN). Being a standard practice in machine learning, we systematically compare the performance of a number of common feature reduction techniques and classifiers to select an optimal combination of a feature reduction technique and a classifier. A cellular database containing 100 manually labelled subsequence is built for evaluating the performance of the classifiers. The generalization error is estimated using the cross validation technique. The experimental results show that CBMM outperforms all other classifies in identifying prophase and has the best overall performance. Conclusion The application of feature reduction techniques can improve the prediction accuracy significantly. CBMM can effectively utilize the contextual information and has the best overall performance when combined with any of the previously mentioned feature reduction techniques.

Abstract Background Owing to rapid expansion of protein structure databases in recent years, methods of structure comparison are becoming increasingly effective and important in revealing novel information on functional properties of proteins and their roles in the grand scheme of evolutionary biology. Currently, the structural similarity between two proteins is measured by the root-mean-square-deviation (RMSD) in their best-superimposed atomic coordinates. RMSD is the golden rule of measuring structural similarity when the structures are nearly identical; it, however, fails to detect the higher order topological similarities in proteins evolved into different shapes. We propose new algorithms for extracting geometrical invariants of proteins that can be effectively used to identify homologous protein structures or topologies in order to quantify both close and remote structural similarities. Results We measure structural similarity between proteins by correlating the principle components of their secondary structure interaction matrix. In our approach, the Principle Component Correlation (PCC) analysis, a symmetric interaction matrix for a protein structure is constructed with relationship parameters between secondary elements that can take the form of distance, orientation, or other relevant structural invariants. When using a distance-based construction in the presence or absence of encoded N to C terminal sense, there are strong correlations between the principle components of interaction matrices of structurally or topologically similar proteins. Conclusion The PCC method is extensively tested for protein structures that belong to the same topological class but are significantly different by RMSD measure. The PCC analysis can also differentiate proteins having similar shapes but different topological arrangements. Additionally, we demonstrate that when using two independently defined interaction matrices, comparison of their maximum eigenvalues can be highly effective in clustering structurally or topologically similar proteins. We believe that the PCC analysis of interaction matrix is highly flexible in adopting various structural parameters for protein structure comparison.

INTRODUCTION: Examining how to deliver primary health care (PHC) services and increase their accessibility (regardless of geographic location) from the patient's perspective is needed. We conducted seven focus groups with people (n = 50) living in rural communities, in British Columbia, Canada, as they reflected on priorities for and use of PHC. METHODS: In addition to discussing their priorities for PHC services, participants completed a brief questionnaire designed to collect information regarding socio-demographics, health status and utilization of primary healthcare providers. Descriptive statistics were obtained from questionnaire data. Focus group data were coded using an evaluation framework specifically developed for PHC; a thematic content analysis was then conducted on the coded data. RESULTS: In total, 80% of participants had been patients of the same provider for more than one year and had an average of two chronic conditions. Participants described the challenges posed by geographical location in terms of: (1) making tradeoffs; (2) management, information, and relationship continuity of care; and (3) efficiency with health care delivery. Additional out-of-pocket expenses were associated with traveling to regional centers for health services. Those living in rural communities, especially people needing additional health services to manage their health problems, made tradeoffs between their safety of having to travel during times of poor road conditions and having their healthcare needs met. CONCLUSION: Challenges to timely access to a regular healthcare provider, continuity of information and management of people's chronic disease conditions, and linkages to specialist services and diagnostic tests pose challenges for those living in rural communities. The geographic location of rural communities compounds the extent to which these people are able to access timely and continuous PHC. [ABSTRACT FROM AUTHOR]

OBJECTIVE: Our objective in this study was to examine how family social-support expectations have changed among older Chinese and Korean U.S. immigrants. METHODS: Fifty-two Cantonese- and Korean-speaking immigrants older than 60 years participated in eight focus groups. Transcripts were translated into English. Themes were developed based on a coding structure and compared to past research. RESULT: Participants discussed changed perspectives of family social support and the need to integrate both American and Chinese or Korean culture, thus becoming bicultural. Three distinct perspectives of family emerged: (1) participants felt they had become peripheral family members, (2) parents were no longer authority figures in families, and (3) participants were more independent. Finally, participants described how factors such as a changed economic environment, living alone, and extending their social network beyond family, promoted a move to biculturalism. DISCUSSION: These results suggest that the integration of two cultures, or biculturalism, is an indicator of successful adaptation to immigration later in life; older Chinese and Korean immigrants are adjusting to living in the United States and blending multiple cultures simultaneously. Thus, acculturation frameworks implying a linear process may not be theoretically valid as ethnic identity, particularly for those who immigrate to different countries, changes over the life course. [ABSTRACT FROM AUTHOR]

Background: Existing literature overlooks the role of gender and race on research productivity, particularly in the context of primary care research. This study examines how gender and race influence the research productivity of primary care researchers in Canada, addressing a gap in existing literature., Methods: Qualitative, descriptive methods were used, involving 60-min interviews with 23 Canadian primary care researchers. 13 participants were female (57%) and 10 participants (43%) were male. Fourteen participants were White (non-racialized; 61%), 8 were racialized (35%) and 1 did not comment on race (4%). Reflexive thematic analysis captured participant perceptions of factors influencing research productivity, including individual, professional, institutional, and systemic aspects., Findings: Systemic bias and institutional culture, including racism, sexism, and unconscious biases against racialized women, emerge as key barriers to research productivity. The parenting life stage further compounds these biases. Barriers include lack of representation in faculty roles, toxic work environments, research productivity metrics, and exclusion by colleagues. Participants indicated that institutional reforms and systemic interventions are needed to foster a diverse, equitable, and inclusive environment. Strategies include recruiting equity-focused leaders, increasing representation of racialized female faculty, diversity training, mentorship programs, providing meaningful support, flexible work arrangements, and protected research time. Sponsors can offer more targeted grants for female and racialized researchers. Adjusting metrics for gender, race, parenthood, and collaborative metrics is proposed to enhance diversity and inclusion among researchers., Interpretation: This study underscores the importance of addressing systemic bias at institutional and systemic levels to create a fair and supportive environment for primary care researchers. A multitude of strategies are needed including increasing representation of racialized female faculty, creating supportive and psychologically safe work environments, and public reporting of data on faculty composition for accreditation and funding decisions. Together, these strategies can alleviate the triple whammy and free these researchers from the Sisyphus Punishment - the absurdity of being asked to climb a hill while pushing a boulder with no hope of reaching the top., Funding: College of Family Physicians of Canada., Competing Interests: Dr. Monica Aggarwal and Dr. Sabrina Wong have no conflicts to declare., (© 2024 The Author(s).)

Introduction: Case management (CM) is among the most studied effective models of integrated care for people with complex needs. The goal of this study is to scale up and assess CM in primary healthcare for people with complex needs., Methods and Analysis: The research questions are: (1) which mechanisms contribute to the successful scale-up of CM for people with complex needs in primary healthcare?; (2) how do contextual factors within primary healthcare organisations contribute to these mechanisms? and (3) what are the relationships between the actors, contextual factors, mechanisms and outcomes when scaling-up CM for people with complex needs in primary healthcare? We will conduct a mixed methods Canadian interprovincial project in Quebec, New-Brunswick and Nova Scotia. It will include a scale-up phase and an evaluation phase. At inception, a scale-up committee will be formed in each province to oversee the scale-up phase. We will assess scale-up using a realist evaluation guided by the RAMESES checklist to develop an initial programme theory on CM scale-up. Then we will test and refine the programme theory using a mixed-methods multiple case study with 10 cases, each case being the scalable unit of the intervention in a region. Each primary care clinic within the case will recruit 30 adult patients with complex needs who frequently use healthcare services. Qualitative data will be used to identify contexts, mechanisms and certain outcomes for developing context-mechanism-outcome configurations. Quantitative data will be used to describe patient characteristics and measure scale-up outcomes., Ethics and Dissemination: Ethics approval was obtained. Engaging researchers, decision-makers, clinicians and patient partners on the study Steering Committee will foster knowledge mobilisation and impact. The dissemination plan will be developed with the Steering Committee with messages and dissemination methods targeted for each audience., Competing Interests: Competing interests: None declared., (© Author(s) (or their employer(s)) 2024. Re-use permitted under CC BY-NC. No commercial re-use. See rights and permissions. Published by BMJ.)

Background: The aim of the current pilot study was to evaluate the usability, acceptability, and tolerability of virtual reality (VR)-based cognitive stimulation exercises (CSEs) in healthy young versus old populations before health care integration. A secondary aim was to assess the accuracy of VR games as a proxy for cognitive stimulation, specifically for attention. VR-based CSEs promise to improve attention and brain function through varied learning systems. Methods: This is a Phase 1 feasibility clinical trial at a single center. It involves 30 healthy volunteers randomly selected using the American Society of Anesthesiologists (ASA) physical status classification system. Participants fall into ASA 1 (age >18-35 years, n = 15) or ASA 2 (age >60 years, n = 15) categories. All participants tested the ReCognitionVR-based CSEs. Feasibility criterion: Participants in each group were monitored for completion of 20 minutes of VR-based CSEs. Acceptability criterion: Proportion of participants with system usability scale (SUS) >35 or SUS score of 87.5. Safety (tolerability) monitoring: Sessions were monitored for neurological, cardiovascular, or pulmonary adverse events (AEs). Safety criterion: No more than 10% of sessions stopped due to neurological, cardiovascular, or pulmonary AEs. Results: The primary outcome (feasibility) of ReCognitionVR-based CSEs was 100%. For the secondary outcome (acceptability), there was no group difference in SUS scores (ASA 1 = 88.17 ± 12.83 vs. ASA 2 = 88.39 ± 10.22, P = 0.81). For the tertiary outcome (safety), mild transient uneasiness was reported by two (13.4%) ASA 1 participants (resolved in 2 minutes), and one (6.67%) ASA 1 participant experienced a temporary >20% increase in blood pressure from baseline. No ASA 2 participants had AEs. Conclusion: The feasibility, acceptability, and safety of ReCognitionVR-based CSEs in healthy elderly volunteers are acceptable, indicating that the evaluation of the ReCognitionVR-based CSEs in hospitalized patients is reasonable.

This poster presents the use of Interpretive Description in ontology development. The methods selected attended to the need for quality and rigour.

Background: Inappropriate or overuse of antibiotic prescribing in primary care highlights an opportunity for antimicrobial stewardship (AMS) programs aimed at reducing unnecessary use of antimicrobials through education, policies and practice audits that optimize antibiotic prescribing. Evidence from the early part of the pandemic indicates a high rate of prescribing of antibiotics for patients with COVID-19. It is crucial to surveil antibiotic prescribing by primary care providers from the start of the pandemic and into its endemic stage to understand the effects of the pandemic and better target effective AMS programs., Methods: This was a matched pair population-based cohort study that used electronic medical record (EMR) data from the Canadian Primary Care Sentinel Surveillance Network (CPCSSN). Participants included all patients that visited their primary care provider and met the inclusion criteria for COVID-19, respiratory tract infection (RTI), or non-respiratory or influenza-like-illness (negative). Four outcomes were evaluated (a) receipt of an antibiotic prescription; (b) receipt of a non-antibiotic prescription; (c) a subsequent primary care visit (for any reason); and (d) a subsequent primary care visit with a bacterial infection diagnosis. Conditional logistic regression was used to evaluate the association between COVID-19 and each of the four outcomes. Each model was adjusted for location (rural or urban), material and social deprivation, smoking status, alcohol use, obesity, pregnancy, HIV, cancer and number of chronic conditions., Results: The odds of a COVID-19 patient receiving an antibiotic within 30 days of their visit is much lower than for patients visiting for RTI or for a non-respiratory or influenza-like-illnesses (AOR = 0.08, 95% CI[0.07, 0.09] compared to RTI, and AOR = 0.43, 95% CI[0.38, 0.48] compared to negatives). It was found that a patient visit for COVID-19 was much less likely to have a subsequent visit for a bacterial infection at all time points., Conclusions: Encouragingly, COVID-19 patients were much less likely to receive an antibiotic prescription than patients with an RTI. However, this highlights an opportunity to leverage the education and attitude change brought about by the public health messaging during the COVID-19 pandemic (that antibiotics cannot treat a viral infection), to reduce the prescribing of antibiotics for other viral RTIs and improve antibiotic stewardship., (© 2024. The Author(s).)

Information on tropical Asian vertebrates has traditionally been sparse, particularly when it comes to cryptic species inhabiting the dense forests of the region. Vertebrate populations are declining globally due to land-use change and hunting, the latter frequently referred as "defaunation." This is especially true in tropical Asia where there is extensive land-use change and high human densities. Robust monitoring requires that large volumes of vertebrate population data be made available for use by the scientific and applied communities. Camera traps have emerged as an effective, non-invasive, widespread, and common approach to surveying vertebrates in their natural habitats. However, camera-derived datasets remain scattered across a wide array of sources, including published scientific literature, gray literature, and unpublished works, making it challenging for researchers to harness the full potential of cameras for ecology, conservation, and management. In response, we collated and standardized observations from 239 camera trap studies conducted in tropical Asia. There were 278,260 independent records of 371 distinct species, comprising 232 mammals, 132 birds, and seven reptiles. The total trapping effort accumulated in this data paper consisted of 876,606 trap nights, distributed among Indonesia, Singapore, Malaysia, Bhutan, Thailand, Myanmar, Cambodia, Laos, Vietnam, Nepal, and far eastern India. The relatively standardized deployment methods in the region provide a consistent, reliable, and rich count data set relative to other large-scale pressence-only data sets, such as the Global Biodiversity Information Facility (GBIF) or citizen science repositories (e.g., iNaturalist), and is thus most similar to eBird. To facilitate the use of these data, we also provide mammalian species trait information and 13 environmental covariates calculated at three spatial scales around the camera survey centroids (within 10-, 20-, and 30-km buffers). We will update the dataset to include broader coverage of temperate Asia and add newer surveys and covariates as they become available. This dataset unlocks immense opportunities for single-species ecological or conservation studies as well as applied ecology, community ecology, and macroecology investigations. The data are fully available to the public for utilization and research. Please cite this data paper when utilizing the data., (© 2024 The Authors. Ecology published by Wiley Periodicals LLC on behalf of The Ecological Society of America.)

Immune therapy is the new frontier of cancer treatment. Therapeutic radiation is a known inducer of immune response and can be limited by immunosuppressive mediators including cyclooxygenase-2 (COX2) that is highly expressed in aggressive triple negative breast cancer (TNBC). A clinical cohort of TNBC tumors revealed poor radiation therapeutic efficacy in tumors expressing high COX2. Herein, we show that radiation combined with adjuvant NSAID (indomethacin) treatment provides a powerful combination to reduce both primary tumor growth and lung metastasis in aggressive 4T1 TNBC tumors, which occurs in part through increased antitumor immune response. Spatial immunological changes including augmented lymphoid infiltration into the tumor epithelium and locally increased cGAS/STING1 and type I IFN gene expression were observed in radiation-indomethacin-treated 4T1 tumors. Thus, radiation and adjuvant NSAID treatment shifts "immune desert phenotypes" toward antitumor M1/TH1 immune mediators in these immunologically challenging tumors. Importantly, radiation-indomethacin combination treatment improved local control of the primary lesion, reduced metastatic burden, and increased median survival when compared with radiation treatment alone. These results show that clinically available NSAIDs can improve radiation therapeutic efficacy through increased antitumor immune response and augmented local generation of cGAS/STING1 and type I IFNs.

Objective: To describe the citation impact and characteristics of Canadian primary care researchers and research publications., Design: Citation analysis., Setting: Canada., Participants: A total of 266 established Canadian primary care researchers., Main Outcome Measures: The 50 most cited primary care researchers in Canada were identified by analyzing data from the Scopus database. Various parameters, including the number of publications and citations, research themes, Scopus h index, content analysis, journal impact factors, and field-weighted citation impact for their publications, were assessed. Information about the characteristics of these researchers was collected using the Google search engine., Results: On average, the 50 most cited primary care researchers produced 51.1 first-author publications (range 13 to 249) and were cited 1864.32 times (range 796 to 9081) over 29 years. Twenty-seven publications were cited more than 500 times. More than half of the researchers were men (60%). Most were clinician scientists (86%) with a primary academic appointment in family medicine (86%) and were affiliated with 5 universities (74%). Career duration was moderately associated with the number of first-author publications (0.35; P =.013). Most research focused on family practice, while some addressed health and health care issues (eg, continuing professional education, pharmaceutical policy)., Conclusion: Canada is home to a cadre of primary care researchers who are highly cited in the medical literature, suggesting that their work is of high quality and relevance. Building on this foundation, further investments in primary care research could accelerate needed improvements in Canadian primary care policy and practice., (Copyright © 2024 the College of Family Physicians of Canada.)

Background: The generation of research evidence and knowledge in primary health care (PHC) is crucial for informing the development and implementation of interventions and innovations and driving health policy, health service improvements, and potential societal changes. PHC research has broad effects on patients, practices, services, population health, community, and policy formulation. The in-depth exploration of the definition and measures of research impact within PHC is essential for broadening our understanding of research impact in the discipline and how it compares to other health services research., Objective: The objectives of the study are (1) to understand the conceptualizations and measures of research impact within the realm of PHC and (2) to identify methodological frameworks for evaluation and research impact and the benefits and challenges of using these approaches. The forthcoming review seeks to guide future research endeavors and enhance methodologies used in assessing research impact within PHC., Methods: The protocol outlines the rapid review and environmental scan approach that will be used to explore research impact in PHC and will be guided by established frameworks such as the Canadian Academy of Health Sciences Impact Framework and the Canadian Health Services and Policy Research Alliance. The rapid review follows scoping review guidelines (PRISMA-ScR; Preferred Reporting Items for Systematic Review and Meta-Analysis Extension for Scoping Reviews). The environmental scan will be done by consulting with professional organizations, academic institutions, information science, and PHC experts. The search strategy will involve multiple databases, citation and forward citation searching, and manual searches of gray literature databases, think tank websites, and relevant catalogs. We will include gray and scientific literature focusing explicitly on research impact in PHC from high-income countries using the World Bank classification. Publications published in English from 1978 will be considered. The collected papers will undergo a 2-stage independent review process based on predetermined inclusion criteria. The research team will extract data from selected studies based on the research questions and the CRISP (Consensus Reporting Items for Studies in Primary Care) protocol statement. The team will discuss the extracted data, enabling the identification and categorization of key themes regarding research impact conceptualization and measurement in PHC. The narrative synthesis will evolve iteratively based on the identified literature., Results: The results of this study are expected at the end of 2024., Conclusions: The forthcoming review will explore the conceptualization and measurement of research impact in PHC. The synthesis will offer crucial insights that will guide subsequent research, emphasizing the need for a standardized approach that incorporates diverse perspectives to comprehensively gauge the true impact of PHC research. Furthermore, trends and gaps in current methodologies will set the stage for future studies aimed at enhancing our understanding and measurement of research impact in PHC., International Registered Report Identifier (irrid): PRR1-10.2196/55860., (©Monica Aggarwal, Brian G Hutchison, Kristina M Kokorelias, Vivian R Ramsden, Noah M Ivers, Andrew Pinto, Ross E G Uphsur, Sabrina T Wong, Nick Pimlott, Steve Slade. Originally published in JMIR Research Protocols (https://www.researchprotocols.org), 23.04.2024.)

Introduction: Radiotherapy-induced glioblastomas (RIGB) are a well-known late and rare complication of brain irradiation. Yet the clinical, radiological and molecular characteristics of these tumors are not well characterized., Methods: This was a retrospective multicentre study that analysed adult patients with newly diagnosed glioblastoma over a 10-year period. Patients with RIGB were identified according to Cahan's criteria for radiation-induced tumors. A case-control analysis was performed to compare known prognostic factors for overall survival (OS) with an independent cohort of IDH-1 wildtype de novo glioblastomas treated with standard temozolomide chemoradiotherapy. Survival analysis was performed by Cox proportional hazards regression., Results: A total of 590 adult patients were diagnosed with glioblastoma. 19 patients (3%) had RIGB. The mean age of patients upon diagnosis was 48 years ± 15. The mean latency duration from radiotherapy to RIGB was 14 years ± 8. The mean total dose was 58Gy ± 10. One-third of patients (37%, 7/19) had nasopharyngeal cancer and a fifth (21%, 4/19) had primary intracranial germinoma. Compared to a cohort of 146 de novo glioblastoma patients, RIGB patients had a shorter median OS of 4.8 months versus 19.2 months ( p -value: <.001). Over a third of RIGBs involved the cerebellum (37%, 7/19) and was higher than the control group (4%, 6/146; p -value: <.001). A fifth of RIGBs (21%, 3/19) were p MGMT methylated which was significantly fewer than the control group (49%, 71/146; p -value: .01). For RIGB patients (32%, 6/19) treated with re-irradiation, the one-year survival rate was 67% and only 8% for those without such treatment ( p -value: .007)., Conclusion: The propensity for RIGBs to develop in the cerebellum and to be p MGMT unmethylated may contribute to their poorer prognosis. When possible re-irradiation may offer a survival benefit. Nasopharyngeal cancer and germinomas accounted for the majority of original malignancies reflecting their prevalence among Southern Chinese.