THE EFFECT OF STRUCTURE IN SHORT REGIONS OF DNA ON MEASUREMENTS ON SHORT OLIGONUCLEOTIDE MICROARRAY AND ION TORRENT PGM SEQUENCING PLATFORMS

Single-stranded DNA in solution has been studied by biophysicists for many years, as complex structures, both stable and dynamic, form under normal experimental conditions. Stable intra-strand formations affect enzymatic technical processes such as PCR and biological processes such as gene regulation. In the research described here we examined the effect of such structures on two high-throughput genomic assay platforms and whether we could predict the influence of those effects to improve the interpretation of genomic sequencing results. Helical structures in DNA can be composed of interactions across strands or within a strand. Exclusion of the aqueous solvent provides an entropic advantage to more compact structures. Our first experiments were tested whether internal helical regions in one of the two binding partners in a microarray experiment would influence the stability of the complex. Our results are novel and show, from molecular simulations and hybridization experiments, that stable secondary structures on the boundary, when not impinging on the ability of targets to access the probes, stabilize the probe-target hybridization. High-throughput sequencing (HTS) platforms use as templates short single-stranded DNA fragments. We tested the influence of template secondary structure on the fidelity of reads generated using the Ion Torrent PGM platform. It can clearly be seen for targets where hairpin structures are quite long (~20bp) that a high level of mis-calling occurs, particularly of deletions, and that some of these deletions are 20-30 bases long. These deletions are not associated with homopolymers, which are known to cause base mis-calls on the PGM, and the effect of structure on the sequencing reaction, rather than the PCR preparative steps, has not been previously published. As HTS technologies bring the cost of sequencing whole genomes down, a number of unexpected observations have arisen. An example that caught our attention is the prevalence of far more short deletions than had been detected using Sanger methods. The prevalence is particularly high in the Korean genome. Since we showed that helical structures could disrupt the fidelity of base calls on the Ion Torrent we looked at the context of the apparent deletions to determine whether any sequence or structure pattern discriminated them. Starting with the genome provided by Kim et al (1) we selected deletions > 2 bases long from chromosome I of a Korean genome. We created 70 nucleotide fragments centered on the deletion. We simulated the secondary structures using OMP software and then modeled using the Random Forest algorithm in the WEKA modeling package to characterize the relations between the deletions and secondary structures in or around them. After training the model on chromosome I deletions we tested it using chromosome 20 deletions. We show that sequence information alone is not able to predict whether a deletion will occur, while the addition of structural information improves the prediction rates. Classification rates are not yet high: additional data and a more precise structural description are likely needed to train a robust model. We are unable to state which of the structures affect in vitro platforms and which occur in vivo. A comparative genomics approach using 38 genomes recently made available for the CAMDA 2013 competition should provide the necessary information to train separate models if the important features are different in the two cases

Early Maladaptive Schemas and Coping Strategies in Abused Women Seeking Divorce

Coping strategies can lead to a reduction in suffering caused by stressful situations due to the role of initial maladaptive schemas. Therefore, the study of these factors can be effective in investigating the causes of divorce. The present study aimed to investigate the mentioned components in women seeking divorce due to spousal abuse and other women seeking divorce referred to forensic medicine in Ardabil province. The research method used was descriptive causal-comparative. The Young and Brown maladaptive schema questionnaire and the Lazarus and Folkman coping strategies were completed by 100 selected women (50 women seeking divorce due to spousal abuse and 50 women seeking divorce) using purposive sampling. Analysis of variance was used to analyze the data. The results showed that the initial maladaptive schemas of abused women from their husbands were significantly different from other women seeking divorce. Abused women had more maladaptive schemas than women seeking divorce for other reasons. Additionally, coping strategies of abused women from their husbands were significantly different from other women seeking divorce, with other causes being more common. According to the findings, the initial maladaptive schemas were higher among women seeking divorce due to spousal abuse than among other women seeking divorce. However, this study had limitations, including the lack of cooperation from Ardabil forensic clients. To reduce divorce rates, we suggest that skills and training programs related to increasing couples' adaptation practices in cohabitation be taught.‌Keywords Early Maladaptive Schemas, Coping Strategies, Divorce, Abused Women by Husband‌‌IntroductionIn recent decades, global social developments have confronted and threatened the family system with new changes, challenges, issues, and needs. When family functions, such as biological, social, cognitive, and emotional functions, are damaged one after another, their members gradually lose their sense of satisfaction (Kowah, 2015). The gradual decrease in family members' satisfaction first causes psychological rupture and then social rupture. Eventually, it becomes a legal event called a divorce (Oldham, 2017). Therefore, divorce is the most important threat against the foundation of the family (Ghotbi et al., 2004). Divorce is known as one of the most common social harms and its occurrence is increasing in industrial and non-industrial countries (Hezar Jaribi et al., 2017). According to the National Registration Organization, the divorce rate from 2006 to 2013 is more than 16% Has increased (Zareian and Sadidpour, 2017). Also, according to the statistics of the Civil Registration Organization, the number of marriages registered in 1396 compared to 1395, decreased by about 8% (51 thousand cases), while the number of divorces reached about 175 thousand cases, which is the highest number recorded in the history of Iran. (Sadegh Shirazi, 2018).Early maladaptive schemas are emotional and cognitive patterns of self-harm that are formed in the mind at the beginning of growth and development and continue throughout life (Sohrabi, Azami et al, 2014). As can be understood from this definition, schemas do not include the behaviour of individuals, but behavior is part of the coping responses that originate from schemas (Salavati and Yazdandoost, 2015). Early maladaptive schemas are one of the factors that can affect marital satisfaction (Young, Kloseco, & Wisshar, 2003). These schemas can affect a person's perception of various situations, such as sexual dysfunction, and are one of the most important etiological factors in the tendency to risky behaviours (Poliment, Morho-Gronert, 2010). , Affect the ability to feel intimacy and satisfaction from romantic and sexual relationships of couples (Chata and Wischman, 2014).Coping strategies refer to one's activities and efforts to manage problems and emotions and to influence physical and psychological consequences (Summerfield and McCray, 2000). These strategies are generally thought of as mediating variables that are called when experiencing a stressor and express the relationship between the stressor and its outcome (Hosseini et al., 2016). In other words, it is a set of cognitive and behavioural efforts that are used to interpret, interpret and correct a stressful situation and lead to a reduction in suffering (Schmidt et al., 2012). From the point of view of Lazarus and Folkman (Lazarus and Folkman, 1984), confrontation is a dynamic phenomenon that shows the state of a person's cognitive and emotional efforts in the face of stressful factors or consequences. Lazarus states that more important than tension is the concept of coping, which plays an important role in adaptation and incompatibility. Sources of environmental stress, when strong and uncontrollable, affect a person's behaviour and disrupt his performance, and the amount of stress caused by environmental stressors depends on a person's mental judgment about the extent of the threat of stress (Lazarus, 1991). MethodologyThe research method was descriptive causal-comparative. The Young Young (1999) maladaptive schema questionnaire and Lazarus and Folkman coping strategies were completed by 100 selected women (50 women seeking divorce due to spousal abuse and 50 women seeking divorce) using purposive sampling. To analyze the data, an analysis of variance was used. ResultThe results showed that the initial maladaptive schemas of abused women from their husbands were significantly different from other women seeking a divorce so that in abused women it was more than the husband. Also, the coping strategies of abused women from their husbands were significantly different from other women seeking divorce, so it was more common in other women seeking a divorce. According to the findings, the initial maladaptive schemas were higher among women seeking divorce due to spousal abuse than other women seeking divorce. However, this study was accompanied by limitations such as the lack of cooperation of Ardabil forensic clients. It is suggested that skills and training programs related to increasing couples' adaptation practices in cohabitation be taught to reduce divorce rates

Comparison of Benefits from Cardiac Resynchronization Therapy between Patients with Ischemic Cardiomyopathy and Patients with Idiopathic Dilated Cardiomyopathy

Background: Cardiac resynchronization therapy (CRT) is an effective treatment for patients with moderate to severe heart failure. However, 20-30% of patients remain non-responders to CRT. We sought to identify which patients benefit the most from CRT in regard to the etiology of heart failure. Methods: Eighty-three consecutive patients (62 men) who had a biventricular pacemaker inserted at Tehran Heart Center between May 2004 and March 2007 were evaluated retrospectively. The inclusion criteria were comprised of New York Heart Association (NYHA) class III or IV, left ventricular ejection fraction<35%, and QRS>120ms. After 6 months, response was defined as being alive, no hospitalization for cardiac decompensation, and an improvement in NYHA class>1 grade. Results: After 6 months, 60 patients out of the 83 patients were responders. Amongst the 83 patients, 48 had ischemic cardiomyopathy and 35 had non-ischemic cardiomyopathy. A cross-tabulation of response versus etiology showed no significant difference between ischemic versus non-ischemic cardiomyopathy with regard to response to CRT (P=0.322). Conclusion: According to our study, there was no difference in response to CRT between ischemic versus non-ischemic cardiomyopathy at six months’ follow-up

Stomatal vs. genome size in angiosperms: the somatic tail wagging the genomic dog?

12 páginas, 5 figuras, 2 tablas.-- et al.[Background and Aims]: Genome size is a function, and the product, of cell volume. As such it is contingent on ecological circumstance. The nature of ‘this ecological circumstance’ is, however, hotly debated. Here, we investigate for angiosperms whether stomatal size may be this ‘missing link’: the primary determinant of genome size. Stomata are crucial for photosynthesis and their size affects functional efficiency. [Methods]: Stomatal and leaf characteristics were measured for 1442 species from Argentina, Iran, Spain and the UK and, using PCA, some emergent ecological and taxonomic patterns identified. Subsequently, an assessment of the relationship between genome-size values obtained from the Plant DNA C-values database and measurements of stomatal size was carried out. [Key Results]: Stomatal size is an ecologically important attribute. It varies with life-history (woody species < herbaceous species < vernal geophytes) and contributes to ecologically and physiologically important axes of leaf specialization. Moreover, it is positively correlated with genome size across a wide range of major taxa. [Conclusions]: Stomatal size predicts genome size within angiosperms. Correlation is not, however, proof of causality and here our interpretation is hampered by unexpected deficiencies in the scientific literature. Firstly, there are discrepancies between our own observations and established ideas about the ecological significance of stomatal size; very large stomata, theoretically facilitating photosynthesis in deep shade, were, in this study (and in other studies), primarily associated with vernal geophytes of unshaded habitats. Secondly, the lower size limit at which stomata can function efficiently, and the ecological circumstances under which these minute stomata might occur, have not been satisfactorally resolved. Thus, our hypothesis, that the optimization of stomatal size for functional efficiency is a major ecological determinant of genome size, remains unproven.A considerable quantity of the data used in this project was collected during projects funded by respectively NERC (UK), the Research Institute of Forests and Rangelands (RIFR, Iran), Universidad Nacional de Córdoba, Comisión Interministerial de Ciencia y Tecnología (Spain) and the Darwin Initiative for the Survival of Species (DEFRA, UK).Peer reviewe

Stomatal vs. genome size in angiosperms

12 páginas, 5 figuras, 2 tablas.-- et al.[Background and Aims]: Genome size is a function, and the product, of cell volume. As such it is contingent on ecological circumstance. The nature of ‘this ecological circumstance’ is, however, hotly debated. Here, we investigate for angiosperms whether stomatal size may be this ‘missing link’: the primary determinant of genome size. Stomata are crucial for photosynthesis and their size affects functional efficiency. [Methods]: Stomatal and leaf characteristics were measured for 1442 species from Argentina, Iran, Spain and the UK and, using PCA, some emergent ecological and taxonomic patterns identified. Subsequently, an assessment of the relationship between genome-size values obtained from the Plant DNA C-values database and measurements of stomatal size was carried out. [Key Results]: Stomatal size is an ecologically important attribute. It varies with life-history (woody species < herbaceous species < vernal geophytes) and contributes to ecologically and physiologically important axes of leaf specialization. Moreover, it is positively correlated with genome size across a wide range of major taxa. [Conclusions]: Stomatal size predicts genome size within angiosperms. Correlation is not, however, proof of causality and here our interpretation is hampered by unexpected deficiencies in the scientific literature. Firstly, there are discrepancies between our own observations and established ideas about the ecological significance of stomatal size; very large stomata, theoretically facilitating photosynthesis in deep shade, were, in this study (and in other studies), primarily associated with vernal geophytes of unshaded habitats. Secondly, the lower size limit at which stomata can function efficiently, and the ecological circumstances under which these minute stomata might occur, have not been satisfactorally resolved. Thus, our hypothesis, that the optimization of stomatal size for functional efficiency is a major ecological determinant of genome size, remains unproven.A considerable quantity of the data used in this project was collected during projects funded by respectively NERC (UK), the Research Institute of Forests and Rangelands (RIFR, Iran), Universidad Nacional de Córdoba, Comisión Interministerial de Ciencia y Tecnología (Spain) and the Darwin Initiative for the Survival of Species (DEFRA, UK).Peer reviewe