MOTIVATION: Proteins often recognize their interaction partners on the basis of short linear motifs located in disordered regions on proteins' surface. Experimental techniques that study such motifs use short peptides to mimic the structural properties of interacting proteins. Continued development of these methods allows for large-scale screening, resulting in vast amounts of peptide sequences, potentially containing information on multiple protein-protein interactions. Processing of such datasets is a complex but essential task for large-scale studies investigating protein-protein interactions. RESULTS: The software tool presented in this article is able to rapidly identify multiple clusters of sequences carrying shared specificity motifs in massive datasets from various sources and generate multiple sequence alignments of identified clusters. The method was applied on a previously published smaller dataset containing distinct classes of ligands for SH3 domains, as well as on a new, an order of magnitude larger dataset containing epitopes for several monoclonal antibodies. The software successfully identified clusters of sequences mimicking epitopes of antibody targets, as well as secondary clusters revealing that the antibodies accept some deviations from original epitope sequences. Another test indicates that processing of even much larger datasets is computationally feasible. AVAILABILITY AND IMPLEMENTATION: Hammock is published under GNU GPL v. 3 license and is freely available as a standalone program (from http://www.recamo.cz/en/software/hammock-cluster-peptides/) or as a tool for the Galaxy toolbox (from https://toolshed.g2.bx.psu.edu/view/hammock/hammock). The source code can be downloaded from https://github.com/hammock-dev/hammock/releases. CONTACT: muller@mou.cz SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
- MeSH
- Algorithms * MeSH
- Databases, Protein * MeSH
- Epitopes chemistry MeSH
- Protein Interaction Domains and Motifs * MeSH
- Humans MeSH
- Markov Chains MeSH
- Molecular Sequence Data MeSH
- Antibodies, Monoclonal chemistry MeSH
- Peptides chemistry MeSH
- Amino Acid Sequence MeSH
- Sequence Alignment MeSH
- Cluster Analysis MeSH
- Software MeSH
- src Homology Domains MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
Background: Pulmonary ultrasound plays a key role in the diagnosis of pneumothorax in emergency and intensive-care medicine. The lung point sign has been generally considered a pathognomonic diagnostic sign. Recently, several other situations have been published that can mimic the lung point, as well as a few different variants of the true lung point sign. Materials and Methods: Based on years of monitoring the literature and collecting our database of ultrasound findings, we prepared a review of ultrasound findings mimicking the lung point sign and ultrasound variants of the true lung point sign. Results: We present four imitations of the lung point sign (physiological lung point sign, pseudo-lung point sign, bleb point sign, and pleurofascial point sign) and two variants of the true lung point sign (double lung point sign and hydro point sign) documented by images and video records. Conclusions: Knowledge of ultrasound imitations and variants of the lung point sign may increase the reliability of pneumothorax diagnosis and may reduce the risk of performing unindicated interventions.
- Publication type
- Journal Article MeSH
INTRODUCTION: Recent advances in machine learning provide new possibilities to process and analyse observational patient data to predict patient outcomes. In this paper, we introduce a data processing pipeline for cardiogenic shock (CS) prediction from the MIMIC III database of intensive cardiac care unit patients with acute coronary syndrome. The ability to identify high-risk patients could possibly allow taking pre-emptive measures and thus prevent the development of CS. METHODS: We mainly focus on techniques for the imputation of missing data by generating a pipeline for imputation and comparing the performance of various multivariate imputation algorithms, including k-nearest neighbours, two singular value decomposition (SVD)-based methods, and Multiple Imputation by Chained Equations. After imputation, we select the final subjects and variables from the imputed dataset and showcase the performance of the gradient-boosted framework that uses a tree-based classifier for cardiogenic shock prediction. RESULTS: We achieved good classification performance thanks to data cleaning and imputation (cross-validated mean area under the curve 0.805) without hyperparameter optimization. CONCLUSION: We believe our pre-processing pipeline would prove helpful also for other classification and regression experiments.
- Publication type
- Journal Article MeSH
AIM: Animal models of Extracorporeal Cardiopulmonary Resuscitation (ECPR) focusing on neurological outcomes are required to further the development of this potentially life-saving technology. The aim of this review is to summarize current animal models of ECPR. METHODS: A comprehensive database search of PubMed, EMBASE, and Web of Science was undertaken. Full-text publications describing animal models of ECPR between January 1, 2000, and June 30, 2022, were identified and included in the review. Data describing the conduct of the animal models of ECPR, measured variables, and outcomes were extracted according to pre-defined definitions. RESULTS: The search strategy yielded 805 unique reports of which 37 studies were included in the final analysis. Most studies (95%) described using a pig model of ECPR with the remainder (5%) describing a rat model. The most common method for induction of cardiac arrest was a fatal ventricular arrhythmia through electrical stimulation (70%). 10 studies reported neurological assessment of animals using physical examination, serum biomarkers, or electrophysiological findings, however, only two studies described a multimodal assessment. No studies reported the use of brain imaging as part of the neurological assessment. Return of spontaneous circulation was the most reported primary outcome, and no studies described the neurological status of the animal as the primary outcome. CONCLUSION: Current animal models of ECPR do not describe clinically relevant neurological outcomes after cardiac arrest. Further work is needed to develop models that more accurately mimic clinical scenarios and can test innovations that can be translated to the application of ECPR in clinical medicine.
- Publication type
- Journal Article MeSH
- Review MeSH
Increasingly available open medical and health datasets encourage data-driven research with a promise of improving patient care through knowledge discovery and algorithm development. Among efficient approaches to such high-dimensional problems are a number of machine learning methods, which are applied in this paper to pressure ulcer prediction in modular critical care data. An inherent property of many health-related datasets is a high number of irregularly sampled time-variant and scarcely populated features, often exceeding the number of observations. Although machine learning methods are known to work well under such circumstances, many choices regarding model and data processing exist. In particular, this paper address both theoretical and practical aspects related to the application of six classification models to pressure ulcers, while utilizing one of the largest available Medical Information Mart for Intensive Care (MIMIC-IV) databases. Random forest, with an accuracy of 96%, is the best-performing approach among the considered machine learning algorithms.
- Publication type
- Journal Article MeSH
BACKGROUND: MicroRNAs are small non-coding one-stranded RNA molecules that play an important role in the post-transcriptional regulation of genes. Bioinformatic predictions indicate that each miRNA can regulate hundreds of target genes. MicroRNA expression can be associated with various cellular processes leading to the metastasis of malignant tumours including non-small cell lung carcinoma. This review summarizes current knowledge on the role of microRNAs in NSCLC metastasis to the brain and lymph nodes. METHODS: A search of the NCBI/PubMed database for publications on expression levels and the mechanisms of microRNA action in NSCLC metastasis. RESULTS AND CONCLUSION: Dysregulation of microRNAs in NSCLC can be associated with brain and lymph node metastasis. There are differences in microRNA expression profiling between NSCLC with and without metastases but it is currently not possible to reliably predict the site of metastasis in NSCLC. Based on data from RNAmicroarrays, bioinformatics analysis is able to predict the target genes of highlighted microRNAs, providing us with complex information about cancer cell features such as enhanced proliferation, migration and invasion. Such microRNAs may then be knocked-down using siRNAs or substituted with miRNA mimics. RNA microarray profiling may thus be a useful tool to select up- or down-regulated microRNAs. A number of authors suggest that microRNAs could serve as biomarkers and therapeutic targets in the treatment of NSCLC metastasis.
- MeSH
- Down-Regulation MeSH
- Humans MeSH
- Lymphatic Metastasis MeSH
- Neoplasm Metastasis MeSH
- MicroRNAs physiology MeSH
- Cell Line, Tumor MeSH
- Bone Neoplasms secondary MeSH
- Brain Neoplasms secondary MeSH
- Lung Neoplasms etiology MeSH
- Carcinoma, Non-Small-Cell Lung etiology MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Review MeSH
Úvod a cíl: Keramika je směs anorganických nekovových materiálů. Její historie je datována již od paleolitu. Využívá se například k výrobě šperků, nádobí, ve stavebním průmyslu, v sochařství a samozřejmě i v zubním lékařství. Keramika je tvrdá, pevná, termicky i elektricky nevodivá, ale je především také estetická. Z důvodu zvyšujících se nároků pacientů na krásný a přirozený úsměv je keramika velmi dobrou volbou při zhotovování estetických protetických prací. Dentální keramika totiž velmi dobře opticky napodobuje tvrdé zubní tkáně, dentin a sklovinu. Proto se dentální keramika stala běžně používaným materiálem v zubních laboratořích. Využívá se ke zhotovení celokeramických, metalokeramických a jádrových korunek či můstků, inlejí, onlejí, estetických faset až po fixtury a suprakonstrukce dentálních implantátů. Ve výběru dentální keramiky pro požadovanou keramickou práci by neměla figurovat jen estetika budoucí keramické práce, ale důležité je brát v úvahu také mechanické vlastnosti keramiky. Žvýkací síly v ústní dutině se zvětšují směrem od frontálního do laterálního úseku, naopak požadavky na estetiku v tomto směru klesají. Keramika, která je vhodným řešením ve frontálním úseku, nemusí být nutně vhodná do laterálního úseku a naopak. Proto je předmětem našeho sdělení přiblížit, porovnat a klasifikovat některé mechanické vlastnosti keramických materiálů využívaných v zubním lékařství. Metodika: Pro odborné sdělení zaměřené na mechanické vlastnosti keramiky jsme čerpaly údaje z odborných knih a z literatury zabývající se danou tematikou dostupné v databázi PubMed. Tyto studie byly následně kriticky hodnoceny pro potřeby odborného sdělení. Závěr: Znalost mechanických vlastností dentálních materiálů je klíčová. Díky této znalosti může stomatolog zvolit vhodný materiál, který nejlépe splňuje konkrétní požadavky pro danou práci. Neznalost těchto vlastností může na druhou stranu vést k neuspokojivému výsledku až selhání práce.
Introduction, aim: Ceramic is a mixture of inorganic nonmetallic materials. The history of the ceramic is dated since Paleolithic age. It is used, for example for production of jewelry, dishes, the construction industry, sculpturing and of course in dentistry. Ceramic is hard, strong, thermal and electrical nonconductive and it has an aesthetic appearance. Due to increasing patient's demands for beautiful and natural smile, the ceramic is a good choice for this aesthetics work. The ceramic mimics very well the optical features of hard dental tissues such as enamel and dentin. Therefore, ceramic becomes a material, which is used every day in dental labs. It is used for production of all-ceramic, porcelain fused to metal (PFM), and core crowns or bridges, inlays, onlays, aesthetic veneers, and also fixtures and supra-constructions of dental implants. The selection of ceramic for the required ceramic work should not only include the aesthetics of the future ceramic work, it is also important to consider mechanical properties of the ceramic. Occlusion forces increase in the oral cavity from frontal to lateral segment while the demands for aesthetics decrease in this direction. The ceramics which is a suitable solution for frontal segment, might not be suitable for lateral segment and vice versa. That is why the objective of our paper is to describe, compare and classify some mechanical properties of ceramic used in dentistry. Methods: For our review focused on mechanical properties of ceramics we collected the relevant data from specialized books and literature dealing with the topic of ceramic available in the PubMed database. These studies were critically evaluated for this review. Conclusion: The knowledge of mechanical properties of dental ceramic is crucial. Thanks to this knowledge, dentist can choose suitable material, which best meets specific requirements for dental restoration. On the other hand, the ignorance can lead to unsatisfactory results up to failure of dental restoration.
- MeSH
- Humans MeSH
- Dental Materials chemistry MeSH
- Denture, Partial, Fixed MeSH
- Dental Porcelain * chemistry MeSH
- Check Tag
- Humans MeSH
- Publication type
- Research Support, Non-U.S. Gov't MeSH
- Review MeSH
Importance: There are inconsistencies in concept, criteria, practice, and documentation of brain death/death by neurologic criteria (BD/DNC) both internationally and within countries. Objective: To formulate a consensus statement of recommendations on determination of BD/DNC based on review of the literature and expert opinion of a large multidisciplinary, international panel. Process: Relevant international professional societies were recruited to develop recommendations regarding determination of BD/DNC. Literature searches of the Cochrane, Embase, and MEDLINE databases included January 1, 1992, through April 2020 identified pertinent articles for review. Because of the lack of high-quality data from randomized clinical trials or large observational studies, recommendations were formulated based on consensus of contributors and medical societies that represented relevant disciplines, including critical care, neurology, and neurosurgery. Evidence Synthesis: Based on review of the literature and consensus from a large multidisciplinary, international panel, minimum clinical criteria needed to determine BD/DNC in various circumstances were developed. Recommendations: Prior to evaluating a patient for BD/DNC, the patient should have an established neurologic diagnosis that can lead to the complete and irreversible loss of all brain function, and conditions that may confound the clinical examination and diseases that may mimic BD/DNC should be excluded. Determination of BD/DNC can be done with a clinical examination that demonstrates coma, brainstem areflexia, and apnea. This is seen when (1) there is no evidence of arousal or awareness to maximal external stimulation, including noxious visual, auditory, and tactile stimulation; (2) pupils are fixed in a midsize or dilated position and are nonreactive to light; (3) corneal, oculocephalic, and oculovestibular reflexes are absent; (4) there is no facial movement to noxious stimulation; (5) the gag reflex is absent to bilateral posterior pharyngeal stimulation; (6) the cough reflex is absent to deep tracheal suctioning; (7) there is no brain-mediated motor response to noxious stimulation of the limbs; and (8) spontaneous respirations are not observed when apnea test targets reach pH <7.30 and Paco2 ≥60 mm Hg. If the clinical examination cannot be completed, ancillary testing may be considered with blood flow studies or electrophysiologic testing. Special consideration is needed for children, for persons receiving extracorporeal membrane oxygenation, and for those receiving therapeutic hypothermia, as well as for factors such as religious, societal, and cultural perspectives; legal requirements; and resource availability. Conclusions and Relevance: This report provides recommendations for the minimum clinical standards for determination of brain death/death by neurologic criteria in adults and children with clear guidance for various clinical circumstances. The recommendations have widespread international society endorsement and can serve to guide professional societies and countries in the revision or development of protocols and procedures for determination of brain death/death by neurologic criteria, leading to greater consistency within and between countries.
- MeSH
- Apnea diagnosis MeSH
- Biomedical Research MeSH
- Diagnosis, Differential MeSH
- Coma diagnosis MeSH
- Humans MeSH
- Brain Death diagnosis physiopathology MeSH
- Brain Stem physiopathology MeSH
- Nervous System Physiological Phenomena * MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Consensus Development Conference MeSH
- Practice Guideline MeSH
Východiská: Zručnosť v interpersonálnej komunikácii ako súčasti suportívnej liečby v onkológii nadobúda nové rozmery po tom, čo sa podarilo demonštrovať pozitívny vplyv komunikácie na zvýšenú schopnosť pacientov vyrovnávať sa s nádorovou chorobou, viac dôverovať ošetrujúcemu personálu, akceptovať záťažovú terapiu a redukovať emocionálny stres a psychosociálnu záťaž. Z hľadiska efektívnej komunikácie cielenej na potreby pacienta je popri empatii potrebné osvojiť si percepčné a behaviorálne schopnosti v komunikácii s onkologickým pacientom. Lekári, zdravotné sestry a onkologickí sociálni pracovníci musia získať schopnosť aktívne počúvať pacienta a niekedy chápať i jeho neochotu rozprávať o svojich obavách a ťažkostiach . Cieľom predloženej práce bolo vypracovať metaanalýzu údajov o princípoch a metodách asertívnej komunikácie s onkologickým pacientom ako formy suportívnej terapie pri zvládaní jeho emocionálnych a sociálnych dysfunkcií. Materiál a metódy: Údaje o interpersonálnej komunikačnej zručnosti v onkológii uvádzané v súčasnej literatúre boli získané z elektronických databáz a boli spracované formou metaanalýzy výsledkov prezentovaných v 24 vybraných publikácií. Výsledky: Aktívny behaviorálny prístup znamená porozumieť aj neverbálnym indikátorom strachu, neistote, podráždenosti, depresie a apatie, ktoré sa zračia v jeho mimike a gestách. Odhalenie týchto a ďalších príčin emocionálnej dysfunkcie (manželské, partnerské a sexuálne problémy, zmeny fyzickej a sociálnej funkčnosti a i.) je základným predpokladom pre poskytnutie účinnej psychosociálnej podpory. Zručnosti v interpersonálnej komunikácii možno získať klinickou praxou a teoretickou prípravou. Záver: Onkologickí zdravotnícki pracovníci by si mali osvojiť pravidlá percepčnej a behaviorálnej komunikácie už počas vysokoškolských štúdií. Avšak zaradenie programu výučby princípov komunikačných zručností do študijných programov medicíny, ošetrovateľstva a sociálnej práce je stále ešte iba v plienkach, napriek tomu, že klinická prax jasne ukázala, že profesionálna forma komunikácie s onkologickým pacientom i členmi jeho rodiny má priaznivý vplyv na pacienta i na samotný liečebný proces, potvrdený vedeckým výskumom a skúsenosťou klinických onkológov.
Background: Interpersonal communication skills as part of the supportive care in cancer won new dimensions by demonstrating the association with enhanced ability of patients to cope with the disease, to enhance trust in health care providers, compliance with treatment and to reduce emotional distress and psychosocial burden. Besides empathy the effective patient‑centered communication is based upon perceptual and behavioral skills of caregivers. Doctors, nurses, and oncology social workers have to achieve skills to listen to patient’s complains and to respond to his/her support needs. The aim of the present paper was to perform a meta‑analysis of published data dealing with principles and methods of the assertive doctor‑patient communication within the supportive care of patients suffering from emotional and social dysfunctions. Material and methods: The data of interpersonal communication skills in oncology presented in the current literature were collected using electronic databases and were elaborated in form of meta‑analysis of 24 selected publications. Results: Active behavioral approach involves the understanding of the non‑verbal indications of patient’s needs, preferences, and expectations, the evaluation of patient’s non‑verbal expression of fear, uncertainty, irritability, depression and apathy or even the unwillingness to disclose his/her concerns. Recognizing these and other concerns (marital and sexual problems, physical and cognitive functioning etc.), caregivers should respond these concerns in verbal form of psychosocial support. Skills in the interpersonal communication can be learned by clinical experience and theoretical preparation. Conclusion: Developing the communication skills including the perception and behavioral style is particularly important in clinician’s early medical teaching. The implementation of communication skills into undergraduate and postgraduate study programs in medicine, nursing, and other paramedical subjects is still in infancy, although the professional communication with cancer patient and its family members is associated with clear and important outcomes of care approved by clinical research and recognized by cancer professionals.
