Intermediates in the Protein Folding Process: A Computational Model

The paper presents a model for simulating the protein folding process in silico. The two-step model (which consists of the early stage—ES and the late stage—LS) is verified using two proteins, one of which is treated (according to experimental observations) as the early stage and the second as an example of the LS step. The early stage is based solely on backbone structural preferences, while the LS model takes into account the water environment, treated as an external hydrophobic force field and represented by a 3D Gauss function. The characteristics of 1ZTR (the ES intermediate, as compared with 1ENH, which is the LS intermediate) confirm the link between the gradual disappearance of ES characteristics in LS structural forms and the simultaneous emergence of LS properties in the 1ENH protein. Positive verification of ES and LS characteristics in these two proteins (1ZTR and 1ENH respectively) suggest potential applicability of the presented model to in silico protein folding simulations

Overtraining syndrome - what we already know

Introduction: Overtraining syndrome (OTS) is a state of excess sportsmen's overload caused by too high an intensity of training. The main cause of OTS is too big a training load. Also, they are other risk factors like restrictive diets, inordinate stress, and inflated expectations of a family and a coach. Description of the state of knowledge: despite numerous hypotheses like dysregulation of hypothalamus and pituitary, inflammatory hypothesis, and glycogen hypothesis the exact cause of OTS is not fully understood. None of these hypotheses explains completely all of the symptoms. In diagnosis, several laboratory tests are required to exclude other diseases. After it, because of possible systemic character diagnostic process of OTS is still problematic. One of the diagnostic methods relies on the measurement of hormone levels. Another potential diagnostic method is the measurement of saliva immunoglobulins and other anti-viral proteins. Also, the measurement of serum cell-free DNA can be used. After the onset of OTS, the most important treatment method is rest, which should last for 6-12 weeks or longer. Nowadays, treatment options are looking for shortenings this time. These options are anti-inflammatory drugs and repeated hypoxia-hyperoxia exposure combined with low-intensity training. Since the only well-established treatment method is prolonged rest, prevention is the most important aspect of OTS management. Adequate education of young athletes and their parents is also important. Summary: Overtraining syndrome is a serious problem that concerns many athletes. This problem not only affects results and careers but also sportsmen’s life. Because of the wide scope of symptoms, which can be often nonspecific making the correct diagnosis can be difficult

Prevalence and factors associated with depressive symptoms among Polish dentistry students

Introduction and objective. Depression is a disease that affects over 264 million people worldwide. According to research, the problem of depression concerns dentistry students. The aim of the research was to investigate the prevalence and severity of depressive symptoms among Polish dental students, determine factors associated with this phenomenon and examine the relationship between these factors and depressive symptoms. Material and method. The participants of the study were dental students enrolled in each of the 10 Polish universities that offer dental education. The research tool was an author’s questionnaire and a Polish-language version of 9-Item-Patient Health Questionnaire (PHQ-9).  Results. A total of 247 dental students took part in the study. The statistical analysis showed that 53.85% of the respondents were provisionally diagnosed with major depression. 8.91% of the participants had symptoms of severe depression. The research suggests that not doing sports regularly and not getting enough sleep are factors associated with depression among Polish dental students. Conclusions. Depressive symptoms among Polish dental students are common. Results suggest that it is important for students to maintain physical activity and take care of proper sleep hygiene. Further research needs to be done in order to explore more factors associated with depressive symptoms in the above-mentioned group

Adverse Childhood Experiences and worsened social relationships in adult life among Polish medical and dental students

Introduction and purpose. Adverse Childhood Experiences (ACEs) are potentially traumatic events experienced before the age of 18 that have lasting negative effects on physical and mental health. Numerous studies have shown that exposure to Adverse Childhood Experiences increases the probability of chronic health conditions, such as obesity, diabetes, coronary heart disease, asthma, depression or PTSD. The aim of the study was to investigate the prevalence of Adverse Childhood Experiences among medical and dental students of Polish Medical Universities and to examine an association between ACEs and chosen factors associated with social relationships of the students.Material and method. A total of 1162 medical and dental students from each year of education and 18 different Polish universities took part in the study. The research tool contained the Adverse Childhood Experiences standardized questionnaire and authors’ questions.Results. More than a half of the students (57.4%) had at least 1 exposure to ACEs. 8.43% of them experienced 4 or more childhood adversities. The most commonly reported ACEs were: emotional neglect (23.06%), emotional abuse (22.98%) and mental illness or a suicide attempt in a household member (21.86%). An overall graded relationship was found between ACE score and: parents’ lower level of education, negative relationship with parents, siblings and friends and having a diagnosis of depression.Conclusions. Adverse Childhood Experiences are common among Polish medical and dental students and are associated with worsened social relationships and depression in adult life of the students. It is important to implement strategies that aim to prevent ACEs and help to build social support networks for those that are affected by them

Chronic traumatic encephalopathy – current state of knowledge

Introduction and purpose. Chronic traumatic encephalopathy (CTE) is a tauopathy caused by repetitive, mild head injuries. It is characterized by perivascular accumulation of hyperphosphorylated tau protein in the neurons and astrocytes. CTE leads to changes in central nervous system, both on microscopic and macroscopic level. The aim of the study was to present the current knowledge on chronic traumatic encephalopathy among athletes, its predisposing factors, symptoms and consequences, as well as diagnostic methods and treatment.Description. CTE occurs among contact sport players, such as American football, ice hockey, soccer, baseball, box and MMA (mixed martial arts), as well as among soldiers and victims of domestic violence. Repetitive head injuries and long career duration increase the risk of CTE. Symptoms of chronic traumatic encephalopathy include a commonly occurring triad: cognitive disturbances, behavioral problems and mood disturbances. Other symptoms include memory loss, parkinsonism, headaches, speech and walking problems. Currently, the only diagnostic method of CTE is a posthumous detection of neuropathological markers. Methods such as detection of exosomal tau protein in plasma and imaging techniques give hope to diagnose CTE in alive patients. Treatment methods of CTE, such as LIPUS (low intensity pulsed ultrasound) therapy are currently being developed.Conclusions. Chronic traumatic encephalopathy among athletes is a serious problem that affects multiple people due to the popularity of contact sports. Thus, an emphasis should be put on prevention, raising awareness and appropriate protection of athletes through changes in regulations and improvement of protective equipment

Depression among Polish medical students and its lifestyle-linked predictors

Introduction and objective. Depression is a common mental disorder that affects over 264 million people worldwide. Medical students are at a particularly high risk of this disease. The aim of the study was to investigate the prevalence of depression among Polish medical students and to determine predictors of this disease that are related to student’s lifestyle. Material and method. A total of 1023 medical students took part in the study. The research tool included a Polish version of the PHQ-9 questionnaire and author’s questions which concerned sociodemographic characteristics of the investigated group and analyzed factors. Answers were collected in the April of 2020. Results. About a half of the students (51.61%, 95% CI: 48.50 – 54.72) were found to have major depression (PHQ score ≥ 10). 30.21% of the students had mild depressive symptoms, 26.00% – moderate depressive symptoms and 15.05% – moderately severe depressive symptoms. 10.56% of the participants had symptoms of severe depression. A statistically significant relationship was found between major depression and: frequent feelings of loneliness, not doing sports regularly, not getting enough sleep, not participating in social meetings often enough, having problems with maintaining stable body weight, using alcohol in order to relieve stress or negative emotions and being non-religious. Conclusions. Depression among medical students in Poland is common. There are many lifestyle-linked predictors which are associated with this disease in the above-mentioned group. It is crucial to take actions aimed at reducing the high prevalence rates of depression among medical students in Poland, such as introducing routine screening for depression and creating resources that would enable students to obtain help

The aqueous environment as an active participant in the protein folding process

© 2018 The Authors Existing computational models applied in the protein structure prediction process do not sufficiently account for the presence of the aqueous solvent. The solvent is usually represented by a predetermined number of H2O molecules in the bounding box which contains the target chain. The fuzzy oil drop (FOD) model, presented in this paper, follows an alternative approach, with the solvent assuming the form of a continuous external hydrophobic force field, with a Gaussian distribution. The effect of this force field is to guide hydrophobic residues towards the center of the protein body, while promoting exposure of hydrophilic residues on its surface. This work focuses on the following sample proteins: Engrailed homeodomain (RCSB: 1enh), Chicken villin subdomain hp-35, n68h (RCSB: 1yrf), Chicken villin subdomain hp-35, k65(nle), n68h, k70(nle) (RCSB: 2f4k), Thermostable subdomain from chicken villin headpiece (RCSB: 1vii), de novo designed single chain three-helix bundle (a3d) (RCSB: 2a3d), albumin-binding domain (RCSB: 1prb) and lambda repressor-operator complex (RCSB: 1lmb)

Adverse Childhood Experiences as a significant predictor of worsened well-being among Polish medical and dental students

Introduction and purpose. Adverse Childhood Experiences (ACEs) are a major public health problem. The aim of the study was to investigate the prevalence of Adverse Childhood Experiences among medical and dental students in Poland and to examine a relationship between ACEs and chosen factors associated with well-being of the students.Material and method. The research tool consisted of the Adverse Childhood Experiences standardized questionnaire and authors’ questions. 934 medical students and 228 dental students took part in the study (a total of 1162 participants). The respondents came from 18 Polish universities.Results. 57.40% of the students experienced at least 1 childhood adversity, 8.43% of them were affected by 4 or more ACEs. The most common adverse childhood experiences were: emotional neglect (23.06%), emotional abuse (22.98%) and mental illness or a suicide attempt in a household member (21.86%). On average, women experienced more childhood adversities than men. An overall graded relationship was found between ACEs and: frequent feelings of loneliness, low self-assessment of academic performance, problems with maintaining stable body weight, reaching for alcohol in order to de-stress and being non-religious.Conclusions. Adverse Childhood Experiences are common among Polish medical and dental students and are linked with multiple aspects of worsened well-being of the students. The study emphasizes a need to create strategies that aim to educate on Adverse Childhood Experiences in order to prevent them and help those who are affected by them

Prediction of Functional Sites Based on the Fuzzy Oil Drop Model

A description of many biological processes requires knowledge of the 3-D structure of proteins and, in particular, the defined active site responsible for biological function. Many proteins, the genes of which have been identified as the result of human genome sequencing, and which were synthesized experimentally, await identification of their biological activity. Currently used methods do not always yield satisfactory results, and new algorithms need to be developed to recognize the localization of active sites in proteins. This paper describes a computational model that can be used to identify potential areas that are able to interact with other molecules (ligands, substrates, inhibitors, etc.). The model for active site recognition is based on the analysis of hydrophobicity distribution in protein molecules. It is shown, based on the analyses of proteins with known biological activity and of proteins of unknown function, that the region of significantly irregular hydrophobicity distribution in proteins appears to be function related

NA61/SHINE online noise filtering using machine learning methods

The NA61/SHINE is a high-energy physics experiment operating at the SPS accelerator at CERN. The physics program of the experiment was recently extended, requiring a significant upgrade of the detector setup. The main goal of the upgrade is to increase the event flow rate from 80Hz to 1kHz by exchanging the read-out electronics of the NA61/SHINE main tracking detectors (Time-Projection-Chambers - TPCs). As the amount of collected data will increase significantly, a tool for online noise filtering is needed. The standard method is based on the reconstruction of tracks and removal of clusters which do not belong to any particle trajectory. However, this method takes a substantial amount of time and resources. A novel approach based on machine learning methods is presented in this proceedings