Extraction of consensus protein patterns in regions containing non-proline cis peptide bonds and their functional assessment

<p>Abstract</p> <p>Background</p> <p>In peptides and proteins, only a small percentile of peptide bonds adopts the <it>cis </it>configuration. Especially in the case of amide peptide bonds, the amount of <it>cis </it>conformations is quite limited thus hampering systematic studies, until recently. However, lately the emerging population of databases with more 3D structures of proteins has produced a considerable number of sequences containing non-proline <it>cis </it>formations (<it>cis</it>-nonPro).</p> <p>Results</p> <p>In our work, we extract regular expression-type patterns that are descriptive of regions surrounding the <it>cis</it>-nonPro formations. For this purpose, three types of pattern discovery are performed: i) exact pattern discovery, ii) pattern discovery using a chemical equivalency set, and iii) pattern discovery using a structural equivalency set. Afterwards, using each pattern as predicate, we search the Eukaryotic Linear Motif (ELM) resource to identify potential functional implications of regions with <it>cis</it>-nonPro peptide bonds. The patterns extracted from each type of pattern discovery are further employed, in order to formulate a pattern-based classifier, which is used to discriminate between <it>cis</it>-nonPro and <it>trans</it>-nonPro formations.</p> <p>Conclusions</p> <p>In terms of functional implications, we observe a significant association of <it>cis</it>-nonPro peptide bonds towards ligand/binding functionalities. As for the pattern-based classification scheme, the highest results were obtained using the structural equivalency set, which yielded 70% accuracy, 77% sensitivity and 63% specificity.</p

The impact of immediate breast reconstruction on the time to delivery of adjuvant therapy: the iBRA-2 study

Background: Immediate breast reconstruction (IBR) is routinely offered to improve quality-of-life for women requiring mastectomy, but there are concerns that more complex surgery may delay adjuvant oncological treatments and compromise long-term outcomes. High-quality evidence is lacking. The iBRA-2 study aimed to investigate the impact of IBR on time to adjuvant therapy. Methods: Consecutive women undergoing mastectomy ± IBR for breast cancer July–December, 2016 were included. Patient demographics, operative, oncological and complication data were collected. Time from last definitive cancer surgery to first adjuvant treatment for patients undergoing mastectomy ± IBR were compared and risk factors associated with delays explored. Results: A total of 2540 patients were recruited from 76 centres; 1008 (39.7%) underwent IBR (implant-only [n = 675, 26.6%]; pedicled flaps [n = 105,4.1%] and free-flaps [n = 228, 8.9%]). Complications requiring re-admission or re-operation were significantly more common in patients undergoing IBR than those receiving mastectomy. Adjuvant chemotherapy or radiotherapy was required by 1235 (48.6%) patients. No clinically significant differences were seen in time to adjuvant therapy between patient groups but major complications irrespective of surgery received were significantly associated with treatment delays. Conclusions: IBR does not result in clinically significant delays to adjuvant therapy, but post-operative complications are associated with treatment delays. Strategies to minimise complications, including careful patient selection, are required to improve outcomes for patients

Breast cancer management pathways during the COVID-19 pandemic: outcomes from the UK ‘Alert Level 4’ phase of the B-MaP-C study

Abstract: Background: The B-MaP-C study aimed to determine alterations to breast cancer (BC) management during the peak transmission period of the UK COVID-19 pandemic and the potential impact of these treatment decisions. Methods: This was a national cohort study of patients with early BC undergoing multidisciplinary team (MDT)-guided treatment recommendations during the pandemic, designated ‘standard’ or ‘COVID-altered’, in the preoperative, operative and post-operative setting. Findings: Of 3776 patients (from 64 UK units) in the study, 2246 (59%) had ‘COVID-altered’ management. ‘Bridging’ endocrine therapy was used (n = 951) where theatre capacity was reduced. There was increasing access to COVID-19 low-risk theatres during the study period (59%). In line with national guidance, immediate breast reconstruction was avoided (n = 299). Where adjuvant chemotherapy was omitted (n = 81), the median benefit was only 3% (IQR 2–9%) using ‘NHS Predict’. There was the rapid adoption of new evidence-based hypofractionated radiotherapy (n = 781, from 46 units). Only 14 patients (1%) tested positive for SARS-CoV-2 during their treatment journey. Conclusions: The majority of ‘COVID-altered’ management decisions were largely in line with pre-COVID evidence-based guidelines, implying that breast cancer survival outcomes are unlikely to be negatively impacted by the pandemic. However, in this study, the potential impact of delays to BC presentation or diagnosis remains unknown

Οικονομική και κοινωνικο-πολιτιστική περιφερειακή ανάπτυξη στην Ελλάδα - Θεσσαλία

Η ανάπτυξη είναι το πιο ενδιαφέρον θέμα και πρόβλημα στον σύγχρονο κόσμο και κατέχει την σημαντικότερη θέση στην οικονομική και κοινωνικοπολιτική σκέψη. Οι στατιστικές, με τους αμείλικτους αριθμούς τους, δίνουν ψυχρά την εικόνα του “παράδεισου” της εποχής μας και πείθουν για την… ανάπτυξη της σημερινής ανθρωπότητας, σε παγκόσμια κλίμακα, αφού ετησίως: 570 εκατομμύρια άνθρωποι υποσιτίζονται, 25 εκατομμύρια πεθαίνουν από πείνα, ενώ 450 δισεκατομμύρια δολάρια πάνε στους εξοπλισμούς! (1979). Στην παρούσα μελέτη ασχολούμαι με την ανάπτυξη της Ελλάδας, προσπαθώντας να δώσω απάντηση στο ερώτημα: Πού βρίσκεται σήμερα η Ελλάδα, από αναπτυξιακή άποψη, με βάση τους επίσημους αριθμούς των έγκυρων στατιστικών; Στόχος πρωταρχικός της διατριβής είναι να αναζητηθούν & προταθούν «ορθολογικές κατευθύνσεις αναπτυξιακών προοπτικών», γεγονός που επετεύχθη με την αμέριστη και πολύτιμη βοήθεια και συνδρομή του επιστημονικού καθοδηγητή μου, ακαδημαϊκού, Profes. Univers. Dr Docient N.N. Constantinescu.Στο πόνημα καταδεικνύεται το «πώς» και το «γιατί» η Ελλάδα είναι χώρα περιφερειακή μέσου επιπέδου ανάπτυξης, με οξυμένες ενδοπεριφερειακές και διαπεριφερειακές ανισότητες και που ανήκει στην περιφέρεια του παγκόσμιου καπιταλιστικού συστήματος. Τα στατιστικά δεδομένα είναι της περιόδου 1950-1980, και μέσα από αυτά –και την ανάλυσή τους– προκύπτουν οι εξελίξεις όλων των τομέων της ελληνικής οικονομίας και κοινωνίας, και κατά συνέπεια συντίθενται και οι προτάσεις, που κατά την άποψή μου μπορούν να συμβάλουν στην επίλυση των υφιστάμενων προβλημάτων

Quality of life of ulcerative colitis patients treated surgically with proctocolectomy and J-pouch formation: a comparative study before surgery and after closure of the defunctioning ileostomy

Background Ulcerative colitis (UC) is a lifelong disease with a relapse-remission pattern that affects patients&apos; social and psychological wellbeing. Restorative proctocolectomy and J-pouch formation is the gold-standard surgical procedure in cases where symptoms are refractory to currently available medical treatment. The aim of this study was to assess patients&apos; quality of life (QoL) in order to evaluate the efficiency of surgery and patients&apos; symptomatology. Methods We performed a prospective comparative study of the QoL of 47 patients with UC, treated surgically. As research tools, we used the Inflammatory Bowel Disease Questionnaire (IBDQ) and the Cleveland Global Quality of Life (CGQL) questionnaire. Parametric and nonparametric tests were used in order to correlate areas of QoL and other selected factors, such as marital status, sex, age, and education. Results The mean scores before and after closure of the ileostomy were 153.29 and 178 for the IBDQ (P=0.0025), and 17.4 and 23.42 for the CGQL (P&lt;0.001), suggesting an overall improvement in QoL. The research showed that there was no specific QoL factor, such as intestinal, systemic, emotional or social life symptoms, that improved significantly more than the others (P=0.99). The IBDQ showed that patients aged less than 20 years (P&lt;0.001), female patients (P=0.03) and patients with secondary education (P&lt;0.001) reported the greatest improvement. Conclusions The QoL in UC patients treated surgically improved following closure of the defunctioning ileostomy. QoL studies are encouraged to optimize and maintain high standards of surgical care, and they could potentially be used for assessment of therapeutic efficacy

Multimodal Lip-Reading for Tracheostomy Patients in the Greek Language

Voice loss constitutes a crucial disorder which is highly associated with social isolation. The use of multimodal information sources, such as, audiovisual information, is crucial since it can lead to the development of straightforward personalized word prediction models which can reproduce the patient’s original voice. In this work we designed a multimodal approach based on audiovisual information from patients before loss-of-voice to develop a system for automated lip-reading in the Greek language. Data pre-processing methods, such as, lip-segmentation and frame-level sampling techniques were used to enhance the quality of the imaging data. Audio information was incorporated in the model to automatically annotate sets of frames as words. Recurrent neural networks were trained on four different video recordings to develop a robust word prediction model. The model was able to correctly identify test words in different time frames with 95% accuracy. To our knowledge, this is the first word prediction model that is trained to recognize words from video recordings in the Greek language

A Sensor-Based Perspective in Early-Stage Parkinson’s Disease: Current State and the Need for Machine Learning Processes

Parkinson’s disease (PD) is a progressive neurodegenerative disorder associated with dysfunction of dopaminergic neurons in the brain, lack of dopamine and the formation of abnormal Lewy body protein particles. PD is an idiopathic disease of the nervous system, characterized by motor and nonmotor manifestations without a discrete onset of symptoms until a substantial loss of neurons has already occurred, enabling early diagnosis very challenging. Sensor-based platforms have gained much attention in clinical practice screening various biological signals simultaneously and allowing researchers to quickly receive a huge number of biomarkers for diagnostic and prognostic purposes. The integration of machine learning into medical systems provides the potential for optimization of data collection, disease prediction through classification of symptoms and can strongly support data-driven clinical decisions. This work attempts to examine some of the facts and current situation of sensor-based approaches in PD diagnosis and discusses ensemble techniques using sensor-based data for developing machine learning models for personalized risk prediction. Additionally, a biosensing platform combined with clinical data processing and appropriate software is proposed in order to implement a complete diagnostic system for PD monitoring

Effectiveness and Quality of life in asthmatic patients treated with budesonide/formoterol via Elpenhaler® device in primary care. The “SKIRON” real world study.

Aim Inhaled corticosteroid (ICS)/long-acting β2 agonist (LABA) combination therapy is used for the effective control of asthma. Aim of this study was to collect data on the effectiveness, safety, quality of life, and patient satisfaction from a fixed dose combination of budesonide/formoterol administered with the Elpenhaler® device following 3-months’ treatment. Methods A 3-month real-life, multicentre, one-arm, prospective observational study (SKIRON study-NCT03055793) was conducted, using the following questionnaires: Asthma Control Questionnaire (ACQ-6) for asthma control assessment, MiniAQLQ questionnaire for QoL assessment, and Feeling of Satisfaction with Inhaler questionnaire (FSI-10) for patients’ satisfaction with the inhaler device. Comorbidities and safety data were also recorded during the study. Results We enrolled 1,174 asthmatic patients following standard clinical practice in primary care from 126 sites in urban and rural areas of Greece. The majority of patients (71.5%) had at least one comorbidity. A statistically significant improvement in the ACQ-6 score was noted at 3 months compared to the baseline evaluation (mean ± SD 2.19 ± 0.97 at baseline vs. 0.55 ± 0.56 at 3 months; mean change -1.64 (95%CI -1.69, -1.57), p ® device. Conclusions In this large real-world study of inadequately-controlled asthma patients in primary care settings, the treatment with budesonide/formoterol FDC with the Elpenhaler® device was associated with significant improvement in patients' asthma control and quality of life.</p