AbstractFluorescent in situ hybridization (FISH) allows researchers to visualize the spatial position and quantity of nucleic acids in fixed samples. Recently, considerable progress has been made in developing oligonucleotide (oligo)-based FISH methods. These methods have enabled researchers to study the three-dimensional organization of the genome at super-resolution and visualize the spatial patterns of gene expression for thousands of genes in individual cells. While considerable progress has been made in developing new molecular methods that harness complex oligo libraries for FISH, there are few existing computational tools to support the bioinformatics workflows necessary to carry out these experiments. Here, we introduce Paint Server and Homology Optimization Pipeline (PaintSHOP), an interactive platform for the reproducible design of oligo FISH experiments. PaintSHOP enables researchers to identify probes for their experimental targets efficiently, to incorporate additional necessary sequences such as primer pairs, and to easily generate standardized files documenting the design of their libraries. Our platform integrates a machine learning model that quantitatively predicts probe specificity on the genome scale into a dynamic web application that creates ready-to-order probe sets for a wide variety of applications. The goal of this freely available web resource is to democratize and standardize the process of designing complex probe sets for the oligo FISH community. PaintSHOP can be accessed at: paintshop.io

Fluorescence in situ hybridization (FISH) allows researchers to visualize the spatial position and quantity of nucleic acids in fixed samples. Recently, considerable progress has been made in developing oligonucleotide (oligo)-based FISH methods that have enabled researchers to study the three-dimensional organization of the genome at super-resolution and visualize the spatial patterns of gene expression for thousands of genes in individual cells. However, there are few existing computational tools to support the bioinformatics workflows necessary to carry out these experiments utilizing oligo FISH probes. Here, we introduce Paint Server and Homology Optimization Pipeline (PaintSHOP), an interactive platform for the design of oligo FISH experiments. PaintSHOP enables researchers to identify probes for their experimental targets efficiently, to incorporate additional necessary sequences such as primer pairs, and to easily generate files documenting library design. PaintSHOP democratizes and standardizes the process of designing complex probe sets for the oligo FISH community.

Objectives: Considering the importance of assessing the range of phenomena that can change in psychodynamic therapy, and lack of appropriate assessment scale in Persian language, the present study assessed the reliability of the Persian mastery scale. The mastery scale is a comprehensive research tool for assessing a patient's mastery of transference-related interpersonal conflicts during the treatment process. Methods: After preparing the Persian version of the mastery scale through the forward-backward translation process, a sample of 36 relationship episodes was rated by three independent judges. Data were collected in Mashhad, Iran in 2015. The psychometric properties of the instrument, including inter-rater reliability and test-retest analysis were assessed. Results: The test-retest correlations of the 3 judges were (0.80, 0.91 and 0.95), highly significant at P < 0.0001 and the inter-rater reliability indicated a good level of agreement (The ICC (3, 3) 0.84, 95% CI [0.72, 0.90]). Conclusions: The current study has provided evidence that the Persian mastery scale is a reliable instrument for assessing changes in inner capacities and resources through psychodynamic treatments. However, further studies are required to investigate the validity of this scale.

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In situ hybridization (ISH) is a powerful tool for investigating the spatial arrangement of nucleic acid targets in fixed samples. ISH is typically visualized using fluorophores to allow high sensitivity and multiplexing or with colorimetric labels to facilitate co-visualization with histopathological stains. Both approaches benefit from signal amplification, which makes target detection effective, rapid, and compatible with a broad range of optical systems. Here, we introduce a unified technical platform, termed "pSABER", for the amplification of ISH signals in cell and tissue systems. pSABER decorates the in situ target with concatemeric binding sites for a horseradish peroxidase-conjugated oligonucleotide which can then catalyze the massive localized deposition of fluorescent or colorimetric substrates. We demonstrate that pSABER effectively labels DNA and RNA targets, works robustly in cultured cells and challenging formalin fixed paraffin embedded (FFPE) specimens. Furthermore, pSABER can achieve 25-fold signal amplification over conventional signal amplification by exchange reaction (SABER) and can be serially multiplexed using solution exchange. Therefore, by linking nucleic acid detection to robust signal amplification capable of diverse readouts, pSABER will have broad utility in research and clinical settings.

Background and Aim: Thalassemia major is one of the most common chronic genetic diseases in the world and in Iran that can impose many adverse effects on the self and society. Psychologically, patients with thalassemia are under stress. According to the World Health Organization (WHO), suicide is one of the leading causes of death worldwide. It is important to identify the people who have the highest risk factors for suicide. The present research investigates the frequency of thoughts, readiness and suicide attempts in people with thalassemia. Methods: This was a cross-sectional study. Its sample was 150 patients with thalassemia in the age range of 10 to 46 years whom we selected through census by sampling at convenience. We gave to patients a standardized Beck Suicide Thought Assessment Questionnaire. We analyzed the research data using descriptive and inferential statistical tests. Results: From among 150 patients with thalassemia in this study, 57.3% of the respondents were male and 42.7% were female. The results showed that there was a negative and significant relationship between suicide thoughts and attempts and age (-0.234) (P <0.05). The mean prevalence of suicide in men (1.89) was significantly higher compared to women (0.79) (P <0.05). We did not observe significant difference in prevalence of suicide thoughts and attempts between married and single groups with a mean difference (0.69) (P <0.05) and, in different educational groups, no significant difference was reported (P> 0.05). Conclusion: The findings of this research showed that among patients with thalassemia, the prevalence of suicidal ideation has a significant percentage. Since suicidal ideation provides a platform for preparation and attempt to commit suicide, so by providing mental health services and regular screening, we can take an effective step to prevent this problem among patients with thalassemia. Keywords: Thalassemia, Suicidal ideation, Suicide.