Benchmark of algorithms for multiple DNA sequence alignment across livestock species

Background: Due to the growing amount of biological data, it is often necessary to select the most optimal estimation method for DNA sequence alignment across livestock species. One of the most important benches of genomics is to modelling homology between considered DNA sequences. A multiple sequence alignment is a potent tool for molecular and evolutionary biology, and there are several programs and algorithms applicable for this purpose. The purpose of this paper was to study the most commonly used DNA alignment algorithms to select the optimal tool dedicated for short sequences.Methods: Four steps of bioinformatics pipelines were considered to benchmark the algorithms for multiple DNA sequence alignment across livestock species: 1) selection of reference genome sequences of ARS1.2 for cattle, EquCab3.0 for horse and vicPac2 for alpaca with a low E-value using TBLASTn 2) removing gaps for these sequences 3) alignment of obtained sequences using examined algorithms 4) matching the quality of aligned sequences with sequences of reference genomes by more software. The time of computation was archived for the whole analysis. The seven programs were utilized, each based on different alignment algorithms, namely: ClustalO, ClustalW, Kalign, MAFFT, MUSCLE, Probcons and T-Coffee.Results: The result obtained in this study showed that the fastest is progressive algorithms such as Kalign or MUSCLE-FAST. Moreover, the iterative algorithms like MAFFT and MUSCLE revealed a higher quality of the alignment. The T-Coffee and Probcons programs were computational cost-effective; simultaneously, they were generating a medium-quality calculation in a relatively long time. The best quality of alignment was shown by iterative variants of the MAFFT program; however, the speed of the calculations was relatively low. The fastest algorithm was Kalign, making alignment much faster than the competitors, but achieving average results in the quality of the alignment. The average speed ratio concerning the quality of the analyzed algorithms was obtained by the progressive version of MAFFT, NS1.Conclusions: We conclude that the results of this study can be used to re-alignment of variant primers in new livestock genome releases

Evaluation of analytical protocols of alignment mapping tools using high throughput next-generation genome sequencing data

Background: Ever since the development of first next-generation genome sequencer (NGS) in 2005, there are rapid developments of high throughput next-generation genome sequencing (HT-NGS) techniques and tools used in genetics and genomics has become much more comfortable and cheaper. The result is the generation of a massive amount of data sets, requiring detailed analysis, which becomes impossible without the use of appropriate bioinformatics tools. One of the crucial steps in the analysis of NGS data is to map readings to a reference sequence. Although the dominance of Illumina synthesis by sequencing (SBS) technology has been noticeable in recent years, the choice of the tools is hampered and the variety of input data and reference genomes. Moreover, the tools used are crucial for result files and further analysis.Methods: The subject of this paper is the three most frequently used alignment mapping programs, which have functions to allow working with many platforms: BWA, Bowtie2 and SMALT. The task of the tested aligners is to match short sequences coming from NGS with reference sequences. The most popular: BWA and Bowtie2 use for this purpose the Burrows-Wheeler transformation and SMALT maps the sequences using hashing and dynamic programming. The presented paper aimed to compare the quality and efficiency of the alignment mapping programs under examination, due to three criteria: i) the quality of the compared sequences of different lengths and from different platforms; ii) coefficient of wrongly compared sequences; iii) the computational resources used.Results: By comparing the results of the mapping analyses for all the programs used, the least popular SMALT is the best. Obtaining the highest percentage of mapped readings for each platform and maintaining the lowest computational memory usage, turns out to be the most optimal choice.Conclusions: The results presented in this paper can be used to verify and rebuild data analysis pipelines from NGS based so far on other tools. We conclude that by using the tools under appropriate conditions, it is possible to improve the quality of the analyses, speed them up and reduce their cost

The association between affective temperaments and depressive symptoms in a population of medical university students, Poland

BackgroundCompared to their peers, medical students are more exposed to stress, and many present symptoms of depression, making them a group prone to experiencing mental illnesses.ObjectiveThis study investigates a potential link between the occurrence of symptoms of depression and the dominating type of affective temperament in young people studying at a medical university.MethodsOne hundred thirty-four medical students were surveyed using two validated questionnaires; the Polish versions of Beck’s Depression Inventory-II (BDI-II) and the Temperament Evaluation of the Memphis, Pisa, and San Diego Autoquestionnaire (TEMPS-A).ResultsThe data analysis revealed a significant link between symptoms of depression and affective temperaments, most significantly in subjects with an anxious temperament.ConclusionThis study confirms the role of various affective temperaments as a risk factor for mood disorders, specifically depression

Pharmacological Support for the Treatment of Obesity—Present and Future

Obesity is a growing civilization problem, associated with a number of negative health consequences affecting almost all tissues and organs. Currently, obesity treatment includes lifestyle modifications (including diet and exercise), pharmacologic therapies, and in some clinical situations, bariatric surgery. These treatments seem to be the most effective method supporting the treatment of obesity. However, they are many limitations to the options, both for the practitioners and patients. Often the comorbidities, cost, age of the patient, and even geographic locations may influence the choices. The pharmacotherapy of obesity is a fast-growing market. Currently, we have at our disposal drugs with various mechanisms of action (directly reducing the absorption of calories—orlistat, acting centrally—bupropion with naltrexone, phentermine with topiramate, or multidirectional—liraglutide, dulaglutide, semaglutide). The drugs whose weight-reducing effect is used in the course of the pharmacotherapy of other diseases (e.g., glucose-sodium cotransporter inhibitors, exenatide) are also worth mentioning. The obesity pharmacotherapy is focusing on novel therapeutic agents with improved safety and efficacy profiles. These trends also include an assessment of the usefulness of the weight-reducing properties of the drugs previously used for other diseases. The presented paper is an overview of the studies related to both drugs currently used in the pharmacotherapy of obesity and those undergoing clinical trials, taking into account the individual approach to the patient

Towards Facilities for Modeling and Synthesis of Architectures for Resource Allocation Problem in Systems Engineering

International audienceExploring architectural design space is often beyond human capacity and makes architectural design a difficult task. Model-based systems engineering must include assistance to the system designer in identifying candidate architectures to subsequently analyze trade-offs. Unfortunately, existing languages and approaches do not incorporate this concern, generally favoring solution analysis over exploring a set of candidate architectures. In this paper, we explore the advantages of designing and configuring the variability problem to solve one of the problems of exploring (synthesizing) candidate architectures in systems engineering: the resource allocation problem. More specifically, this work reports on the use of the Clafer modeling language and its gateway to the CSP Choco Solver, on an industrial case study of heterogeneous hardware resource allocation (GPP-GPGPU-FPGA). Based on experiments on the modeling in Clafer, and the impact of its translation into the constraint programming paradigm (per-formance studies), discussions highlight some issues concerning facilities for modeling and synthesis of architectures and recommendations are proposed towards the use of this variability approach

The Structure of Temperament in Caregivers of Patients with Schizophrenia

The onset of schizophrenia symptoms usually occurs in early youth. As a result, the parents of these patients usually become their caregivers. The role of a caregiver for a person with schizophrenia is a considerable mental and physical burden. Therefore, an interesting issue is what motivates these people to take up this challenge. It is probable that, apart from the moral imperative or kinship, the factor determining this decision is the personality structure of the caregiver. The aim of our study was to compare the structure of temperament (according to the model of temperament as formal characteristics of behavior developed by Jan Strelau) in caregivers of young adults (age 18–25 years) with schizophrenia with the structure of temperament of parents of healthy young adults still living in the family home under their care. The study group consisted of 64 people (51 women), who were taking care of young adults (aged 18–25 years) with schizophrenia, while the control group (53 people, 42 women) consisted of parents of healthy adults still living in the family home. Both groups were asked to complete a questionnaire of the authors’ own design on their demographic data as well as The Formal Characteristics of Behavior—Temperament Inventory to assess the temperament traits. The results were given in the number of points obtained on average in each dimension. Both groups did not differ in terms of size and age, with women predominating. Caregivers of young adults with schizophrenia had higher values of briskness (43.22 ± 4.45 vs. 42.90 ± 3.98, p = 0.032), emotional reactivity (46.02 ± 4.39 vs. 41.01 ± 3.12, p = 0.012) and activity level (44.01.89 ± 4.15 vs. 37.59 ± 4.77, p = 0.022) compared to the control group. The remaining dimensions of temperament: perseverance, sensory sensitivity, rhythmicity, and endurance did not differentiate between the two groups. The temperament structure of caregivers of young people with schizophrenia differs from the temperament structure of caregivers of healthy adults. Caregivers of sick people have higher values of briskness, emotional reactivity, and activity level compared to the control group

Metabolic syndrome is associated with similar long-term prognosis in non-obese and obese patients. An analysis of 45 615 patients from the nationwide LIPIDOGRAM 2004-2015 cohort studies

Aims We aimed to evaluate the association between metabolic syndrome (MetS) and long-term all-cause mortality. Methods The LIPIDOGRAM studies were carried out in the primary care in Poland in 2004, 2006 and 2015. MetS was diagnosed based on the National Cholesterol Education Program, Adult Treatment Panel III (NCEP/ATP III) and Joint Interim Statement (JIS) criteria. The cohort was divided into four groups: non-obese patients without MetS, obese patients without MetS, non-obese patients with MetS and obese patients with MetS. Differences in all-cause mortality was analyzed using Kaplan-Meier and Cox regression analyses. Results 45,615 participants were enrolled (mean age 56.3, standard deviation: 11.8 years; 61.7% female). MetS was diagnosed in 14,202 (31%) by NCEP/ATP III criteria, and 17,216 (37.7%) by JIS criteria. Follow-up was available for 44,620 (97.8%, median duration 15.3 years) patients. MetS was associated with increased mortality risk among the obese (hazard ratio, HR: 1.88 [95% CI, 1.79-1.99] and HR: 1.93 [95% CI 1.82-2.04], according to NCEP/ATP III and JIS criteria, respectively) and non-obese individuals (HR: 2.11 [95% CI 1.85-2.40] and 1.7 [95% CI, 1.56-1.85] according to NCEP/ATP III and JIS criteria respectively). Obese patients without MetS had a higher mortality risk than non-obese patients without MetS (HR: 1.16 [95% CI 1.10-1.23] and HR: 1.22 [95%CI 1.15-1.30], respectively in subgroups with NCEP/ATP III and JIS criteria applied). Conclusions MetS is associated with increased all-cause mortality risk in non-obese and obese patients. In patients without MetS obesity remains significantly associated with mortality. The concept of metabolically healthy obesity should be revised