Redefining the bacteriophage mv4 site-specific recombination system and the sequence specificity of its attB and core-attP sites

Through their involvement in the integration and excision of a large number of mobile genetic elements, such as phages and integrative and conjugative elements (ICEs), site-specific recombination systems based on heterobivalent tyrosine recombinases play a major role in genome dynamics and evolution. However, despite hundreds of these systems having been identified in genome databases, very few have been described in detail, with none from phages that infect Bacillota (formerly Firmicutes). In this study, we reanalyzed the recombination module of Lactobacillus delbrueckii subsp. bulgaricus phage mv4, previously considered atypical compared with classical systems. Our results reveal that mv4 integrase is a 369 aa protein with all the structural hallmarks of recombinases from the Tn916 family and that it cooperatively interacts with its recombination sites. Using randomized DNA libraries, NGS sequencing, and other molecular approaches, we show that the 21-bp core-attP and attB sites have structural similarities to classical systems only if considering the nucleotide degeneracy, with two 7-bp inverted regions corresponding to mv4Int core-binding sites surrounding a 7-bp strand-exchange region. We also examined the different compositional constraints in the core-binding regions, which define the sequence space of permissible recombination sites.

Apparent simplicity and emergent robustness in the control of the Escherichia coli cell cycle

To examine how bacteria achieve robust cell proliferation across diverse conditions, we developed a method that quantifies 77 cell morphological, cell cycle, and growth phenotypes of a fluorescently labeled Escherichia coli strain and >800 gene deletion derivatives under multiple nutrient conditions. This approach revealed extensive phenotypic plasticity and deviating mutant phenotypes were often nutrient dependent. From this broad phenotypic landscape emerged simple and robust unifying rules (laws) that connect DNA replication initiation, nucleoid segregation, FtsZ ring formation, and cell constriction to specific aspects of cell size (volume, length, or added length) at the population level. Furthermore, completion of cell division followed the initiation of cell constriction after a constant time delay across strains and nutrient conditions, identifying cell constriction as a key control point for cell size determination. Our work provides a population-level description of the governing principles by which E. coli integrates cell cycle processes and growth rate with cell size to achieve its robust proliferative capability. A record of this paper's transparent peer review process is included in the supplemental information.

DNA Segregation in Enterobacteria

DNA segregation ensures that cell offspring receive at least one copy of each DNA molecule, or replicon, after their replication. This important cellular process includes different phases leading to the physical separation of the replicons and their movement toward the future daughter cells. Here, we review these phases and processes in enterobacteria with emphasis on the molecular mechanisms at play and their controls.

Spatial-temporal simulation for hospital infection spread and outbreaks of Clostridioides difficile

Validated and curated datasets are essential for studying the spread and control of infectious diseases in hospital settings, requiring clinical information on patients' evolution and their location. The literature shows that approaches based on Artificial Intelligence (AI) in the development of clinical-support systems have benefits that are increasingly recognized. However, there is a lack of available high-volume data, necessary for trusting such AI models. One effective method in this situation involves the simulation of realistic data. Existing simulators primarily focus on implementing compartmental epidemiological models and contact networks to validate epidemiological hypotheses. Nevertheless, other practical aspects such as the hospital building distribution, shifts or safety policies on infections has received minimal attention. In this paper, we propose a novel approach for a simulator of nosocomial infection spread, combining agent-based patient description, spatial-temporal constraints of the hospital settings, and microorganism behavior driven by epidemiological models. The predictive validity of the model was analyzed considering micro and macro-face validation, parameter calibration based on literature review, model alignment, and sensitive analysis with an expert. This simulation model is useful in monitoring infections and in the decision-making process in a hospital, by helping to detect spatial-temporal patterns and predict statistical data about the disease.

Atypical low-copy number plasmid segregation systems, all in one?

Plasmid families harbor different maintenances functions, depending on their size and copy number. Low copy number plasmids rely on active partition systems, organizing a partition complex at specific centromere sites that is actively positioned using NTPase proteins. Some low copy number plasmids lack an active partition system, but carry atypical intracellular positioning systems using a single protein that binds to the centromere site but without an associated NTPase. These systems have been studied in the case of the Escherichia coli R388 and of the Staphylococcus aureus pSK1 plasmids. Here we review these two systems, which appear to be unrelated but share common features, such as their distribution on plasmids of medium size and copy number, certain activities of their centromere-binding proteins, StbA and Par, respectively, as well as their mode of action, which may involve dynamic interactions with the nucleoid-packed chromosome of their hosts.

The use of networks in spatial and temporal computational models for outbreak spread in epidemiology: A systematic review

OBJECTIVES

To examine recent literature in order to present a comprehensive overview of the current trends as regards the computational models used to represent the propagation of an infectious outbreak in a population, paying particular attention to those that represent network-based transmission.

METHODS

a systematic review was conducted following the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines. Papers published in English between 2010 and September 2021 were sought in the ACM Digital Library, IEEE Xplore, PubMed and Scopus databases.

RESULTS

Upon considering their titles and abstracts, 832 papers were obtained, of which 192 were selected for a full content-body check. Of these, 112 studies were eventually deemed suitable for quantitative and qualitative analysis. Emphasis was placed on the spatial and temporal scales studied, the use of networks or graphs, and the granularity of the data used to evaluate the models. The models principally used to represent the spreading of outbreaks have been stochastic (55.36%), while the type of networks most frequently used are relationship networks (32.14%). The most common spatial dimension used is a region (19.64%) and the most used unit of time is a day (28.57%). Synthetic data as opposed to an external source were used in 51.79% of the papers. With regard to the granularity of the data sources, aggregated data such as censuses or transportation surveys are the most common.

CONCLUSION

We identified a growing interest in the use of networks to represent disease transmission. We detected that research is focused on only certain combinations of the computational model, type of network (in both the expressive and the structural sense) and spatial scale, while the search for other interesting combinations has been left for the future.

A Novel Introgression Line Library Derived from a Wild Melon Gives Insights into the Genetics of Melon Domestication, Uncovering New Genetic Variability Useful for Breeding

A collection of 30 melon introgression lines (ILs) was developed from the wild accession Ames 24297 (TRI) into 'Piel de Sapo' (PS) genetic background. Each IL carried an average of 1.4 introgressions from TRI, and the introgressions represented 91.4% of the TRI genome. Twenty-two ILs, representing 75% of the TRI genome, were evaluated in greenhouse (Algarrobo and Meliana) and field (Alcàsser) trials, mainly to study traits related to domestication syndrome such as fruit weight (FW) and flesh content (FFP), as well as other fruit quality traits as fruit shape (FS), flesh firmness (FF), soluble solid concentration (SSC), rind color and abscission layer. The IL collection showed an impressive variation in size-related traits, with FW ranging from 800 to 4100 g, reflecting the strong effect of the wild genome on these traits. Most of the ILs produced smaller fruits compared with PS; however, unexpectedly, the IL TRI05-2 produced bigger fruits, likely due to new epistatic interacions with the PS genetic background. In contrast, the genotypic effect for FS was smaller, and few QTLs with notable effects were detected. Interestingly, variability was also observed for FFP, FF and SSC, rind color and abscission layer formation. Genes in these introgressions are candidates for having been involved in melon domestication and diversification as well. These results confirm that the TRI IL collection is a very powerful tool for mapping traits of agronomic interest in melon, allowing the confirmation of previously reported QTLs and the identification of new ones to better understand the domestication process of this crop.

Meaningful time-related aspects of alerts in Clinical Decision Support Systems. A unified framework

Alerts are a common functionality of clinical decision support systems (CDSSs). Although they have proven to be useful in clinical practice, the alert burden can lead to alert fatigue and significantly reduce their usability and acceptance. Based on a literature review, we propose a unified framework consisting of a set of meaningful timestamps that allows the use of state-of-the-art measures for alert burden, such as alert dwell time, alert think time, and response time. In addition, it can be used to investigate other measures that could be relevant as regards dealing with this problem. Furthermore, we provide a case study concerning three different types of alerts to which the framework was successfully applied. We consider that our framework can easily be adapted to other CDSSs and that it could be useful for dealing with alert burden measurement thus contributing to its appropriate management.

Isoniazid preventive therapy completion in children under 5 years old who are contacts of tuberculosis cases in Lima, Peru: study protocol for an open-label, cluster-randomized superiority trial

BACKGROUND

Children < 5 years old in contact with TB cases are at high risk for developing severe and fatal forms of TB. Contact investigation, BCG vaccination, and isoniazid preventive therapy (IPT) are the most effective strategies to prevent TB among children. However, the implementation of IPT faces challenges at several stages of the cascade of care of TB infection among children, particularly those less than 5 years old. In Peru, a large proportion of children do not complete IPT, which highlights the need to design effective interventions that enhance preventive therapy adherence and completion. Although the body of evidence for such interventions has grown, interventions in medium TB incidence settings are lacking. This study aims to test the effectiveness, acceptability, and feasibility of an intervention package to increase information and motivation to complete IPT among children < 5 who have been prescribed IPT.

METHODS

An open-label, cluster-randomized superiority trial will be conducted in two districts in South Lima, Peru. Thirty health facilities will be randomized as clusters, 10 to the intervention and 20 to control (standard of care). We aim to recruit 10 children from different households in each cluster. Participants will be caretakers of children aged < 5 years old who initiated IPT. The intervention consists of educational material, and short message services (SMS) reminders and motivators. The primary outcomes will be the proportion of children who picked up > 90% of the 24 weeks of IPT (22 pick-ups) and the proportion of children who picked up the 24 weeks of IPT. The standard of care is a weekly pick-up with monthly check-ups in a health facility. Feasibility and acceptability of the intervention will be assessed through an interview with the caretaker.

DISCUSSION

Unfavorable outcomes of TB in young children, high effectiveness of IPT, and low rates of IPT completion highlight the need to enhance adherence and completion of IPT among children < 5 years old. Testing of a context-adapted intervention is needed to improve IPT completion rates and therefore TB prevention in young children.

TRIAL REGISTRATION

ClinicalTrials.gov NCT03881228. Registered on March 19, 2019.

Comparison of the levels of selected specific antibodies in the immunoglobulin G of colostrum versus milk and serum in dairy cows (Bos taurus)

Commercial products containing immunoglobulin G (IgG) sourced from colostrum, milk, and/or serum may be used to supplement or replace maternal colostrum in newborn dairy calves. To determine if antibody specificities in bovine milk and serum IgG differ from colostrum IgG, we sampled serum, colostrum (1 to 2 hours post-partum), and milk (day 5 post-partum) from 24 dairy heifers or cows. Specific antibodies [IgG class (H&L)] to 8 common pathogens were measured using enzyme-linked immunosorbent assays (ELISAs). Immunoglobin G1 and IgG2 subclass-specific ELISAs were performed for 3 of these pathogens. Colostrum-derived IgG contained more specific antibodies to rotavirus [IgG (H&L) and IgG1] and to IgG (H&L) of bovine respiratory syncytial virus (BRSV), bovine parainfluenza-3 virus (BPI₃V), Staphylococcus aureus, Escherichia coli F5 (K99), and bovine coronavirus than milk IgG. Colostral IgG contained more antibodies to BRSV (IgG1), rotavirus (IgG1), and IgG (H&L) specific for BRSV, bovine herpesvirus-1 (BHV-1), BPI₃V, E. coli F5 (K99), and Streptococcus uberis than serum IgG. Compared to serum, milk contained more IgG (H&L) antibody to BRSV, BHV-1, and BPI₃V, IgG1-specific BRSV, and rotavirus. These data indicate that IgG derived from colostrum delivers more specific antibodies to these endemic pathogens of calves compared to IgG sourced from milk or serum. In addition, the IgG1 subclass predominates in milk and colostrum, and both deliver a similar spectrum of antibodies.

Business Process Model and Notation and openEHR Task Planning for Clinical Pathway Standards in Infections: Critical Analysis

Background

Clinical pathways (CPs) are usually expressed by means of workflow formalisms, providing health care personnel with an easy-to-understand, high-level conceptual model of medical steps in specific patient conditions, thereby improving overall health care process quality in clinical practice. From a standardized perspective, the business process model and notation (BPMN), a widely spread general-purpose process formalism, has been used for conceptual modeling in clinical domains, mainly because of its easy-to-use graphical notation, facilitating the common understanding and communication of the parties involved in health care. However, BPMN is not particularly oriented toward the peculiarities of complex clinical processes such as infection diagnosis and treatment, in which time plays a critical role, which is why much of the BPMN clinical-oriented research has revolved around how to extend the standard to address these special needs. The shift from an agnostic, general-purpose BPMN notation to a natively clinical-oriented notation such as openEHR Task Planning (TP) could constitute a major step toward clinical process improvement, enhancing the representation of CPs for infection treatment and other complex scenarios.

Objective

Our work aimed to analyze the suitability of a clinical-oriented formalism (TP) to successfully represent typical process patterns in infection treatment, identifying domain-specific improvements to the standard that could help enhance its modeling capabilities, thereby promoting the widespread adoption of CPs to improve medical practice and overall health care quality.

Methods

Our methodology consisted of 4 major steps: identification of key features of infection CPs through literature review, clinical guideline analysis, and BPMN extensions; analysis of the presence of key features in TP; modeling of relevant process patterns of catheter-related bloodstream infection as a case study; and analysis and proposal of extensions in view of the results.

Results

We were able to easily represent the same logic applied in the extended BPMN-based process models in our case study using out-of-the-box standard TP primitives. However, we identified possible improvements to the current version of TP to allow for simpler conceptual models of infection CPs and possibly of other complex clinical scenarios.

Conclusions

Our study showed that the clinical-oriented TP specification is able to successfully represent the most complex catheter-related bloodstream infection process patterns depicted in our case study and identified possible extensions that can help increase its adequacy for modeling infection CPs and possibly other complex clinical conditions.

Living at the Wrong Time: Effects of Unmatching Official Time in Portugal and Western Spain

Human circadian rhythmicity is subjected to the internal circadian clock, the sun and social clocks (official time, social/work schedules). The discrepancy among these clocks, as occurs when official time does not match its geographical time zone, may produce circadian disruption. Western Spain (GMT+1/+2) and Portugal (GMT0/+1) share similar longitudes (sun time) but have different official times. This provides a unique opportunity to evaluate the effects of official time on circadian rhythmicity and sleep in elderly and retired populations (with no remunerated duties presumed, although other social commitments may be present) at both locations. Although both populations slept enough for their age (7-8 h), circadian robustness (e.g., interdaily stability, relative amplitude) was greater in Portugal, especially during weekdays, while greater desynchronization (both body temperature vs. motor activity and body temperature vs. light exposure) tended to occur in the Spaniards. Once corrected by GMT0, meals took place later in Spain than in Portugal, especially as the day progresses, and a possible interplay between bed/meal timings and internal desynchronization was found. Our results point to the possible deleterious effect on circadian system robustness when official time is misaligned with its geographical time zone.

Clearance and persistence of Escherichia coli in the freshwater mussel Unio mancus

The excessive use of antibiotics has led to the emergence of resistant bacteria, mainly from the Enterobacterales group, with high pathogenic/zoonotic potentials that can lead to problems in public health. The increasing presence in freshwater ecosystems highlights the need to evaluate potential sentinel species as risk indicators for both ecosystem and human health. The freshwater mussels provide several ecosystem services, may represent potential sentinel species due to their ability to filter water and retain both organic and inorganic particles. We tested the capability of U. mancus to retain Escherichia coli as a model bacterial organism. Under experimental conditions, the mussels could clear suspended E. coli, facilitating its rapid elimination from water within the first 24 h after exposure. The species also presented a maximum retention time of 4 days. We also provide allometric equations correlating the filtering capacity with the length and the weight of mussel body parts often used in biometric studies. We provide a first assessment of the potential of the bivalve Unio mancus to act as a sentinel species for the detection of Enterobacterales and demonstrate the ability to act as a water cleaner.

Handling Time Constraints in Infection Clinical Pathways Using openEHR TP

Clinical Pathways (CP) provide healthcare personnel with an easy-to-understand high level model of medical steps in specific patient conditions, thereby improving overall process quality in clinical practice. The emergence of new clinical-oriented standards such as openEHR Task Planning (TP) could pose a major step towards clinical process improvement, particularly in complex domains such as infection diagnosis and treatment, where time plays a critical role. In this work, we analyze the suitability of TP to successfully represent time constraints of common process patterns in infections, modelling some of the Catheter-Related Blood Stream Infection (CR-BSI) process patterns as a case study. Our research shows that TP is useful to represent time constraints of infection CPs, although minor improvements could increase its suitability not only for infection processes but for other time-related complex clinical scenarios.

Interventive psychodiagnosis of children through online orientation of parents in a University Clinical Practice in Brazil: an alternative for underserved populations during the COVID-19 pandemic

Introduction

A private university in Santos offers a free psychological service for assessing and intervening in chilhood psychological problems through a internship program which had to be delivered online due to the COVID-19 pandemic. The interns were only allowed to attend their parents online, instead of their children.

Objectives

Evaluating this new online service is the aim of this work.

Methods

24 parents of 34 children aged 4-10 years were attended by pairs or trios of 52 interns. The were modules made up of assessment, intervention and feedback, using different instruments such as interviews, screening questionnaires and the observation of 5-minute free play in domestic environment and of a family collage through a video recorded by parents. Feedback and intervention happened in various moments. The interns created a storybook using metaphoric narrative as a feedback tool in which a synthesis of the psychodiagnostic process and orientation was presented to the children.

Results

There was progress and decrease or elimination of symptons in 19 of the 34 children. Among the children who did not improve, one of them did not present any difficulties; 7 of them had many absences and the other 7 were referred to further assessment for reasons related to the complexity of their difficulties or a probable unsuitability of the online orientation.

Conclusions

The orientation was helpful for 55,89% of the children, showing to be a valid alternative for families who do not have financial resources for attending private clinics or fail to access public health services or even during social distance measures.

Disclosure

No significant relationships.

Four-month incidence of suicidal thoughts and behaviors among healthcare workers after the first wave of the Spain COVID-19 pandemic

Healthcare workers (HCW) are at high risk for suicide, yet little is known about the onset of suicidal thoughts and behaviors (STB) in this important segment of the population in conjunction with the COVID-19 pandemic. We conducted a multicenter, prospective cohort study of Spanish HCW active during the COVID-9 pandemic. A total of n = 4809 HCW participated at baseline (May-September 2020; i.e., just after the first wave of the pandemic) and at a four-month follow-up assessment (October-December 2020) using web-based surveys. Logistic regression assessed the individual- and population-level associations of separate proximal (pandemic) risk factors with four-month STB incidence (i.e., 30-day STB among HCW negative for 30-day STB at baseline), each time adjusting for distal (pre-pandemic) factors. STB incidence was estimated at 4.2% (SE = 0.5; n = 1 suicide attempt). Adjusted for distal factors, proximal risk factors most strongly associated with STB incidence were various sources of interpersonal stress (scaled 0-4; odds ratio [OR] range = 1.23-1.57) followed by personal health-related stress and stress related to the health of loved ones (scaled 0-4; OR range 1.30-1.32), and the perceived lack of healthcare center preparedness (scaled 0-4; OR = 1.34). Population-attributable risk proportions for these proximal risk factors were in the range 45.3-57.6%. Other significant risk factors were financial stressors (OR range 1.26-1.81), isolation/quarantine due to COVID-19 (OR = 1.53) and having changed to a specific COVID-19 related work location (OR = 1.72). Among other interventions, our findings call for healthcare systems to implement adequate conflict communication and resolution strategies and to improve family-work balance embedded in organizational justice strategies.

A cryptic variation in a member of the Ovate Family Proteins is underlying the melon fruit shape QTL fsqs8.1

The gene underlying the melon fruit shape QTL fsqs8.1 is a member of the Ovate Family Proteins. Variation in fruit morphology is caused by changes in gene expression likely due to a cryptic structural variation in this locus. Melon cultivars have a wide range of fruit morphologies. Quantitative trait loci (QTL) have been identified underlying such diversity. This research focuses on the fruit shape QTL fsqs8.1, previously detected in a cross between the accession PI 124112 (CALC, producing elongated fruit) and the cultivar 'Piel de Sapo' (PS, producing oval fruit). The CALC fsqs8.1 allele induced round fruit shape, being responsible for the transgressive segregation for this trait observed in that population. In fact, the introgression line CALC8-1, carrying the fsqs8.1 locus from CALC into the PS genetic background, produced perfect round fruit. Following a map-based cloning approach, we found that the gene underlying fsqs8.1 is a member of the Ovate Family Proteins (OFP), CmOFP13, likely a homologue of AtOFP1 and SlOFP20 from Arabidopsis thaliana and tomato, respectively. The induction of the round shape was due to the higher expression of the CALC allele at the early ovary development stage. The fsqs8.1 locus showed an important structural variation, being CmOFP13 surrounded by two deletions in the CALC genome. The deletions are present at very low frequency in melon germplasm. Deletions and single nucleotide polymorphisms in the fsqs8.1 locus could not be not associated with variation in fruit shape among different melon accessions, what indicates that other genetic factors should be involved to induce the CALC fsqs8.1 allele effects. Therefore, fsqs8.1 is an example of a cryptic variation that alters gene expression, likely due to structural variation, resulting in phenotypic changes in melon fruit morphology.

Chronodisruption and Ambulatory Circadian Monitoring in Cancer Patients: Beyond the Body Clock

Purpose of Review

Circadian rhythms impose daily rhythms a remarkable variety of metabolic and physiological functions, such as cell proliferation, inflammation, and DNA damage response. Accumulating epidemiological and genetic evidence indicates that circadian rhythms’ disruption may be linked to cancer. The integration of circadian biology into cancer research may offer new options for increasing cancer treatment effectiveness and would encompass the prevention, diagnosis, and treatment of this disease.

Recent Findings

In recent years, there has been a significant development and use of multi-modal sensors to monitor physical activity, sleep, and circadian rhythms, allowing, for the very first time, scaling accurate sleep monitoring to epidemiological research linking sleep patterns to disease, and wellness applications providing new potential applications.

Summary

This review highlights the role of circadian clock in tumorigenesis, cancer hallmarks and introduces the state-of-the-art in sleep-monitoring technologies, discussing the eventual application of insights in clinical settings and cancer research.

Simulating the impact of non-pharmaceutical interventions limiting transmission in COVID-19 epidemics using a membrane computing model

Epidemics caused by microbial organisms are part of the natural phenomena of increasing biological complexity. The heterogeneity and constant variability of hosts, in terms of age, immunological status, family structure, lifestyle, work activities, social and leisure habits, daily division of time and other demographic characteristics make it extremely difficult to predict the evolution of epidemics. Such prediction is, however, critical for implementing intervention measures in due time and with appropriate intensity. General conclusions should be precluded, given that local parameters dominate the flow of local epidemics. Membrane computing models allows us to reproduce the objects (viruses and hosts) and their interactions (stochastic but also with defined probabilities) with an unprecedented level of detail. Our LOIMOS model helps reproduce the demographics and social aspects of a hypothetical town of 10 320 inhabitants in an average European country where COVID-19 is imported from the outside. The above-mentioned characteristics of hosts and their lifestyle are minutely considered. For the data in the Hospital and the ICU we took advantage of the observations at the Nursery Intensive Care Unit of the Consortium University General Hospital, Valencia, Spain (included as author). The dynamics of the epidemics are reproduced and include the effects on viral transmission of innate and acquired immunity at various ages. The model predicts the consequences of delaying the adoption of non-pharmaceutical interventions (between 15 and 45 days after the first reported cases) and the effect of those interventions on infection and mortality rates (reducing transmission by 20, 50 and 80%) in immunological response groups. The lockdown for the elderly population as a single intervention appears to be effective. This modeling exercise exemplifies the application of membrane computing for designing appropriate multilateral interventions in epidemic situations.

Bacterial cell proliferation: from molecules to cells

Bacterial cell proliferation is highly efficient, both because bacteria grow fast and multiply with a low failure rate. This efficiency is underpinned by the robustness of the cell cycle and its synchronization with cell growth and cytokinesis. Recent advances in bacterial cell biology brought about by single-cell physiology in microfluidic chambers suggest a series of simple phenomenological models at the cellular scale, coupling cell size and growth with the cell cycle. We contrast the apparent simplicity of these mechanisms based on the addition of a constant size between cell cycle events (e.g. two consecutive initiation of DNA replication or cell division) with the complexity of the underlying regulatory networks. Beyond the paradigm of cell cycle checkpoints, the coordination between the DNA and division cycles and cell growth is largely mediated by a wealth of other mechanisms. We propose our perspective on these mechanisms, through the prism of the known crosstalk between DNA replication and segregation, cell division and cell growth or size. We argue that the precise knowledge of these molecular mechanisms is critical to integrate the diverse layers of controls at different time and space scales into synthetic and verifiable models.

Using the diagnostic odds ratio to select multivariate sequential patterns in order to build an interpretable pattern-based classifier in a clinical domain (Preprint)

Background

It is important to exploit all available data on patients in settings such as intensive care burn units (ICBUs), where several variables are recorded over time. It is possible to take advantage of the multivariate patterns that model the evolution of patients to predict their survival. However, pattern discovery algorithms generate a large number of patterns, of which only some are relevant for classification.

Objective

We propose to use the diagnostic odds ratio (DOR) to select multivariate sequential patterns used in the classification in a clinical domain, rather than employing frequency properties.

Methods

We used data obtained from the ICBU at the University Hospital of Getafe, where 6 temporal variables for 465 patients were registered every day during 5 days, and to model the evolution of these clinical variables, we used multivariate sequential patterns by applying 2 different discretization methods for the continuous attributes. We compared 4 ways in which to employ the DOR for pattern selection: (1) we used it as a threshold to select patterns with a minimum DOR; (2) we selected patterns whose differential DORs are higher than a threshold with regard to their extensions; (3) we selected patterns whose DOR CIs do not overlap; and (4) we proposed the combination of threshold and nonoverlapping CIs to select the most discriminative patterns. As a baseline, we compared our proposals with Jumping Emerging Patterns, one of the most frequently used techniques for pattern selection that utilizes frequency properties.

Results

We have compared the number and length of the patterns eventually selected, classification performance, and pattern and model interpretability. We show that discretization has a great impact on the accuracy of the classification model, but that a trade-off must be found between classification accuracy and the physicians’ capacity to interpret the patterns obtained. We have also identified that the experiments combining threshold and nonoverlapping CIs (Option 4) obtained the fewest number of patterns but also with the smallest size, thus implying the loss of an acceptable accuracy with regard to clinician interpretation. The best classification model according to the trade-off is a JRIP classifier with only 5 patterns (20 items) that was built using unsupervised correlation preserving discretization and differential DOR in a beam search for the best pattern. It achieves a specificity of 56.32% and an area under the receiver operating characteristic curve of 0.767.

Conclusions

A method for the classification of patients’ survival can benefit from the use of sequential patterns, as these patterns consider knowledge about the temporal evolution of the variables in the case of ICBU. We have proved that the DOR can be used in several ways, and that it is a suitable measure to select discriminative and interpretable quality patterns.

Combination gel of 2% amitriptyline and 0.5% ketamine to treat refractory erythromelalgia pain - a case report of pain control success

Erythromelalgia (EM) is a rare autosomal dominant neuropathy characterized by the combination of severe burning pain and erythematous warm extremities. Chronic pain control is most often unsuccessful and a completely effective therapy is yet to be identified. Recent studies have reported significant improvements in pain management using a combination of amitriptyline and ketamine in a topical formulation. We describe a 1-year follow-up pain control success case of a male patient with EM, proposed for topical use of a 2% Amitriptyline and 0.5% Ketamine gel.

Combination gel of 2% amitriptyline and 0.5% ketamine to treat refractory erythromelalgia pain - a case report of pain control success

Erythromelalgia (EM) is a rare autosomal dominant neuropathy characterized by the combination of severe burning pain and erythematous warm extremities. Chronic pain control is most often unsuccessful and a completely effective therapy is yet to be identified. Recent studies have reported significant improvements in pain management using a combination of amitriptyline and ketamine in a topical formulation. We describe a 1-year follow-up pain control success case of a male patient with EM, proposed for topical use of a 2% Amitriptyline and 0.5% Ketamine gel.

Online psychological therapy for kids during social distancing: A study case in a brazilian clinical setting

Introduction

In response to the spread of COVID-19, many Brazilian therapists faced the challenge of taking their practices online considering legal and ethical issues, besides learning to handle new technologies in a way the therapeutic setting was maintained. The cooperation of the family is fundamental for the creation and maintenance of an adequate therapeutic setting. Children are not sufficiently mature to speak clearly about what bothers them or to talk about how they feel and why, so, drawing, pretend playing, story telling, playing games are the common tools for children’s communication during therapy.

Objectives

Evaluating if online therapy for children can support therapeutic play tools and be effective in a virtual environment preserving the therapeutic setting.

Methods

Two children aged 6 to 11 attended the psychological sessions that were conducted through video calls.The family should provide a silent and private room for those sessions. The children were free to choose the toy they would like to play with and that was available at home such as board games, comic and story books. Mimicry, drawing, an adaptation of the Winnicott Squiggle Game were used, as well as electronic games through screen sharing.

Results

The emotional conflicts were expressed either through conventional games and play or electronic games. Playing with children online was possible as well as maintaining the therapeutic alliance in order to carry on with the treatment in a proper therapeutic setting.

Conclusions

Online therapy for kids showed to be an effective form of service delivery, under strict measures of social distancing in Brazil.

Intervention to promote physical activation and improve sleep and response feeding in infants for preventing obesity early in life, the baby-act trial: Rationale and design

Infant obesity is increasing in the US, particularly among Hispanics. Rapid weight gain during infancy increases the risk of obesity later in life and could be prevented through multi-modal interventions addressing multiple risk factors through population-level programs.

OBJECTIVES

1) determine the extent to which the intervention, compared with the usual care control condition, improves healthy weight gain and specific behaviors (physical activity, sleep, diet) in the first year of life and 2) evaluate the cost of the intervention as a modification of the current WIC standard of care.

METHODS

The lifestyle intervention focuses on age-appropriate infant physical activation, healthy sleep and sedentary patterns, and response feeding, by improving parenting skills delivered through a combination of technology (web-platform and text messages) and phone counseling. It is being tested among caregivers of infant participants of the Puerto Rico WIC program through a cluster-randomized controlled trial in 14 WIC clinics in San Juan starting in pregnancy until the infant is 12 months of age. The main outcome is infant rate of weight gain at 12 months; secondary outcomes include objectively measured hours of infant movement, sedentary behaviors and sleep, diet quality score and response feeding behaviors. We are also recording fees, time and personnel involved in the intervention development, maintenance and dissemination.

CONCLUSIONS

If successful, the intervention could be incorporated as a 'best practice' through WIC policy as a means to strengthen obesity prevention efforts to improve minority health and eliminate health disparities among Hispanics and possibly other at-risk groups beyond the childhood period. Clinicaltrials.gov registration: NCT03517891.

The Retrochiasmal Optic Pathway: A Link in Jeopardy

The case of an intraventricular meningioma is presented and the visual complication incurred by its surgical resection is discussed. The importance of selecting the most optimal surgical approach and the basis for that selection are highlighted.

GEOTECNOLOGIAS APLICADA NOS CONFLITOS DE USO DO SOLO EM ÁREAS DE PRESERVAÇÃO PERMANENTE NO MUNICÍPIO DE BARRA BONITA/SP

As áreas de conflito são definidas pelo mau uso do solo pelo homem e vem causando sérios problemas ao meio ambiente, resultando em desequilíbrio ecológico e desgaste dos recursos naturais, especialmente quando se refere às áreas de preservação permanente, que têm importância fundamental para os ecossistemas de equilíbrio e preservação dos recursos hídricos. O planejamento é um fator chave para o controle dos impactos ambientais ao meio ambiente. As áreas de preservação permanente evitam o assoreamento e erosão proporcionando uma proteção natural, principalmente em áreas das nascentes. Os serviços ambientais prestados auxiliam a proteção da flora e fauna, na preservação dos corredores ecológicos, e na continuação das espécies ali presentes. Este estudo teve por objetivo avaliar os conflitos de uso e ocupação da terra em áreas de Preservação Permanente do município de Barra Bonita/SP, utilizando como base cartográfica, o Sistema de Informação Geográfica (SIG) e imagem de satélite Sentinel 2-A de 2017, em escala 1:10.000. Os resultados mostraram que quase ¾ da área é ocupado com cana-de-açúcar (72,72%) e que as áreas de preservação permanente estão sendo usados inadequadamente por cana-de-açúcar (72,75%). O SIG ArcGis e as técnicas de geoprocessamento demonstraram agilidade e eficiência na identificação, quantificação e edição de mapas de uso do solo, preservação permanente e de conflitos em áreas de preservação permanente.

Non-adhesion to therapy in the elderly, in Tábua

Introduction Most medicines are taken by the elderly because they suffer natural changes, which lead to chronic and degenerative diseases. Older people often have increasingly complex medication regimens, which may lead to errors with dosing and administration and to non-adherence to therapy. Non-adherence to therapy leads to a decrease in therapeutic efficacy, an increase in morbidity, suffering, and health costs. It is influenced by several factors that can and should be driven to improve health status.

Objectives The objective of this study was to determine and evaluate the medication regimen complexity in an elderly population, in Tábua, and verify its relation with adherence to therapy.

Methodology Surveys were applied to elderly people in order to collect the medication data. The study lasted for 5 months and took place at a pharmacy (n = 337). Only people with ≥65 years were included. Medication regimen complexity was assessed using the Brazilian translation for the Medication Regimen Complexity Index (MRCI) and adhesion to therapy was measured by MAT scale. Data was analysed with SPSS statistical program, version 24.0.

Results Our study showed a high percentage of adhesion to therapy (65%) and also of polypharmacy among the elderly (84,9%). Most medication that elderly take belong to the cardiovascular system pharmaceutical group (94,1%). Still, people described some difficulties to adhesion to therapy, mainly forgetfulness (73,66%). Data also revealed that individuals with more literacy and those who are not under polypharmacy showed more adherence to therapy (p = 0.000 and p = 0.012). The most significant result from our study was that MRCI and non-adherence are correlated statistically, that is, a higher MRCI leads to an increase in non-adherence to therapy (p = 0.001).

Conclusion Healthcare professionals should be aware that high levels of medication regimen complexity suggest bad outcomes and non-adherence to therapy. They should assist the elderly, help avoid errors, and find solutions to improve adherence to therapy, whenever possible.

Histopathological hallmarks of cutaneous lesions of capillary malformation-arteriovenous malformation syndrome

IMPORTANCE

Capillary malformation-arteriovenous malformation (CM-AVM) syndrome is a recently described syndrome with distinctive cutaneous lesions. Very little is known about the histopathology of these lesions.

OBJECTIVE

The purpose of the study was to evaluate the histopathological characteristics of the pink macules of the CM-AVM syndrome and to investigate if these pink macules could be classified as capillary malformations or arteriovenous malformations based on their histopathological features.

DESIGN-SETTINGS-PARTICIPANTS

We conducted a retrospective multicenter study involving eight hospitals in Spain. Fifteen biopsies from pink macules of the CM-AVM syndrome were analysed and compared with five biopsies of diverse capillary malformations and three stage I arteriovenous malformations.

RESULTS

Pink macules' biopsies of the CM-AVM syndrome showed similar features including a high vascular density encompassing capillaries and numerous thick-walled arterioles mainly located in the superficial dermis, a predominance of elongated over round vessels, scarce or absent erythrocytes within the lumina and discrete perivascular inflammation. CMs were characterized by an increased number of capillary-type vessels mostly rounded and located in the upper dermis. AVMs were composed by highly increased numbers of vessels with a branching pattern involving the full thickness of the dermis, without erythrocytes within the lumina. Wilms tumour 1 protein was positive in the endothelial cells both in pink macules of the CM-AVM and in arteriovenous malformations.

CONCLUSIONS AND RELEVANCE

Pink macules of the CM-AVM syndrome seem to be different from capillary malformations. Our results suggest that histologically and immunohistochemically they are closer to incipient arteriovenous malformations than to capillary malformations. A deepened knowledge about the nature of these skin lesions will contribute to the better understanding of capillary malformation-arteriovenous malformation syndrome, and will open the possibility of new and more specific treatments in the future.

[COVID-19: how to transform a noninvasive ventilation device in a critical care ventilator]

La pandemia del COVID-19 ha hecho estragos, no solo en el número de víctimas fatales sino también en la infraestructura de los hospitales y unidades de cuidados intensivos. El número limitado de respiradores es una preocupación de toda la comunidad dada la demanda masiva y a muy corto plazo de estos equipos. Esta presentación tiene como fin dar soluciones sencillas para ventilar pacientes intubados de modo mandatorio utilizando equipos de ventilación no invasiva. Las soluciones propuestas permiten 2 estrategias claras frente al COVID-19: Reemplazar las máquinas de anestesia para disponer de ellas en pacientes. Usar la opción de equipos de ventilación no invasiva para pacientes con COVID-19 a modo de «puente» y a la espera de la liberación de un respirador específico en la unidad de cuidados críticos.

DECLIVIDADE E POTENCIAL PARA MECANIZAÇÃO AGRÍCOLA DA BACIA HIDROGRÁFICA DO RIBEIRÃO PEDERNEIRAS - PEDERNEIRAS/SP

A declividade do terreno contribui para o escoamento das águas, pois quanto maior for o trecho em declive, maior será o escoamento da água pela superfície, arrastando outros materiais para os recursos hídricos superficiais, influenciando a qualidade da água e a infiltração e nos processos erosivos fluviais e pluviais, assim como na tipologia da vegetação, bem como contribui para a formação do solo e serve de indicador na definição de áreas de risco e restrição de uso. A declividade dos rios pode ser associada à velocidade do escoamento, transporte de sedimentos e conformação das áreas de preservação permanentes. Este trabalho teve como objetivo analisar a declividade do terreno na bacia hidrográfica do ribeirão Pederneiras, estado de São Paulo e classificá-la quanto as áreas aptas e inaptas à mecanização agrícola. A área de estudo está localizada entre as coordenadas geográficas 22°20' e 22°26' de latitude S e 48°44' e 48°56' de longitude W Gr., situadas nos municípios de Agudos e Pederneiras, do estado de São Paulo, com uma área de 14918,28 ha. Os mapas de declividade foram elaborados por meio de técnicas de geoprocessamento, tendo-se como base cartográfica: as cartas planialtimétricas do Instituto Brasileiro de Geografia e Estatística e a imagem do satélite Sentinel-2 em ambiente de Sistema de Informação Geográfica – ArcGis 10.4.1. As classes de declividade do solo foram classificadas como relevo plano (0 – 3%), suave ondulado (3 – 8%), ondulado (8 – 20%), forte ondulado (20 – 45%), montanhoso (45 – 75%) e escarpado (> 75%) e áreas para mecanização agrícola como aptas (áreas mecanizáveis) e inaptas (áreas não mecanizáveis). Os resultados mostraram que o relevo plano e suavemente ondulado predominou em quase 89% da área, enquadrando-as em áreas aptas à mecanização com pequenas restrições. v

Nucleoid Size Scaling and Intracellular Organization of Translation across Bacteria

The scaling of organelles with cell size is thought to be exclusive to eukaryotes. Here, we demonstrate that similar scaling relationships hold for the bacterial nucleoid. Despite the absence of a nuclear membrane, nucleoid size strongly correlates with cell size, independent of changes in DNA amount and across various nutrient conditions. This correlation is observed in diverse bacteria, revealing a near-constant ratio between nucleoid and cell size for a given species. As in eukaryotes, the nucleocytoplasmic ratio in bacteria varies greatly among species. This spectrum of nucleocytoplasmic ratios is independent of genome size, and instead it appears linked to the average population cell size. Bacteria with different nucleocytoplasmic ratios have a cytoplasm with different biophysical properties, impacting ribosome mobility and localization. Together, our findings identify new organizational principles and biophysical features of bacterial cells, implicating the nucleocytoplasmic ratio and cell size as determinants of the intracellular organization of translation.

Haemodynamic and analgesic control in a perioperative opioid-free approach to bariatric surgery - A case report

New approaches to bariatric surgery aim to achieve stress-free anaesthesia with sympathetic stability to protect organs and provide sufficient tissue perfusion, analgesia and rapid emergence. Opioid-free and multimodal approaches to anaesthesia provide intra- and post-operative sedation and analgesia, particularly advantageous in morbidly obese patients, but their feasibility and efficacy are still disputed. We describe the case of a female patient proposed for laparoscopic bariatric surgery, conducted under an opioid-free anaesthesia protocol, the haemodynamic, ventilatory and analgesic control, and intra- and post-operative monitoring and complications.

Application of Machine Learning Methods to Ambulatory Circadian Monitoring (ACM) for Discriminating Sleep and Circadian Disorders

The present study proposes a classification model for the differential diagnosis of primary insomnia (PI) and delayed sleep phase disorder (DSPD), applying machine learning methods to circadian parameters obtained from ambulatory circadian monitoring (ACM). Nineteen healthy controls and 242 patients (PI = 184; DSPD = 58) were selected for a retrospective and non-interventional study from an anonymized Circadian Health Database (https://kronowizard.um.es/). ACM records wrist temperature (T), motor activity (A), body position (P), and environmental light exposure (L) rhythms during a whole week. Sleep was inferred from the integrated variable TAP (from temperature, activity, and position). Non-parametric analyses of TAP and estimated sleep yielded indexes of interdaily stability (IS), intradaily variability (IV), relative amplitude (RA), and a global circadian function index (CFI). Mid-sleep and mid-wake times were estimated from the central time of TAP-L5 (five consecutive hours of lowest values) and TAP-M10 (10 consecutive hours of maximum values), respectively. The most discriminative parameters, determined by ANOVA, Chi-squared, and information gain criteria analysis, were employed to build a decision tree, using machine learning. This model differentiated between healthy controls, DSPD and three insomnia subgroups (compatible with onset, maintenance and mild insomnia), with accuracy, sensitivity, and AUC >85%. In conclusion, circadian parameters can be reliably and objectively used to discriminate and characterize different sleep and circadian disorders, such as DSPD and OI, which are commonly confounded, and between different subtypes of PI. Our findings highlight the importance of considering circadian rhythm assessment in sleep medicine.

A methodology based on multiple criteria decision analysis for combining antibiotics in empirical therapy

BACKGROUND

The current situation of critical progression in resistance to more effective antibiotics has forced the reuse of old highly toxic antibiotics and, for several reasons, the extension of the indications of combined antibiotic therapy as alternative options to broad spectrum empirical mono-therapy. A key aspect for selecting an appropriate and adequate antimicrobial therapy is that prescription must be based on local epidemiology and knowledge since many aspects, such as prevalence of microorganisms and effectiveness of antimicrobials, change from hospitals, or even areas and services within a single hospital. Therefore, the selection of combinations of antibiotics requires the application of a methodology that provides objectivity, completeness and reproducibility to the analysis of the detailed microbiological, epidemiological, pharmacological information on which to base a rational and reasoned choice.

METHODS

We proposed a methodology for decision making that uses a multiple criteria decision analysis (MCDA) to support the clinician in the selection of an efficient combined empiric therapy. The MCDA includes a multi-objective constrained optimization model whose criteria are the maximum efficacy of therapy, maximum activity, the minimum activity overlapping, the minimum use of restricted antibiotics, the minimum toxicity of antibiotics and the activity against the most prevalent and virulent bacteria. The decision process can be defined in 4 steps: (1) selection of clinical situation of interest, (2) definition of local optimization criteria, (3) definition of constraints for reducing combinations, (4) manual sorting of solutions according to patient's clinical conditions, and (5) selection of a combination.

EXPERIMENTS AND RESULTS

In order to show the application of the methodology to a clinical case, we carried out experiments with antibiotic susceptibility tests in blood samples taken during a five years period at a university hospital. The validation of the results consists of a manual review of the combinations and experiments carried out by an expert physician that has explained the most relevant solutions proposed according to current clinical knowledge and their use.

CONCLUSION

We show that with the decision process proposed, the physician is able to select the best combined therapy according to different criteria such as maximum efficacy, activity and minimum toxicity. A method for the recommendation of combined antibiotic therapy developed on the basis of a multi-objective optimization model may assist the physicians in the search for alternatives to the use of broad-spectrum antibiotics or restricted antibiotics for empirical therapy. The decision proposed can be easily reproduced for any local epidemiology and any different clinical settings.

Validation of a Device for the Ambulatory Monitoring of Sleep Patterns: A Pilot Study on Parkinson's Disease

The development of wearable devices has increase interest in the use of ambulatory methods to detect sleep disorders more objectively than those permitted by subjective scales evaluating sleep quality, while subjects maintain their usual lifestyle. This study aims to validate an ambulatory circadian monitoring (ACM) device for the detection of sleep and wake states and apply it to the evaluation of sleep quality in patients with Parkinson disease (PD). A polysomnographic validation study was conducted on a group of patients with different sleep disorders in a preliminary phase, followed by a pilot study to apply this methodology to PD patients. The ACM device makes it possible to estimate the main sleep parameters very accurately, as demonstrated by: (a) the lack of significant differences between the mean values detected by PSG and ACM in time in bed (TIB), total sleep time (TST), sleep efficiency (SE), and time awake after sleep onset (WASO); (b) the slope of the correlation lines between the parameters estimated by the two procedures, very close to 1, which demonstrates the linearity of the predictions; (c) the low bias value in the estimates obtained through ACM. Sleep in PD is associated with lower distal skin temperature, efficiency and overall sleep time; greater WASO, activity during sleep and duration of naps and a worse circadian function index. In summary, the ACM device has proven to be clinically useful to evaluate sleep in an objective manner, thanks to the integrated management of different complementary variables, having advantages over conventional actigraphy.

MODELO AUTOMÁTICO DE CLASSIFICAÇÃO DE BOVINOS PARA O ABATE VIA REDES NEURAIS ARTIFICIAIS

Hoje em dia, a busca por ferramentas que facilitam e até mesmo substituem o trabalho humano têm ganhado grande destaque mundial. As redes neurais artificiais (RNAs) é uma dessas ferramentas, pois apresentam uma quantidade de aplicações, principalmente quando se trata de classificação de dados, reconhecimento de padrões, análise de imagens, entre outros. Com este intuito, o objetivo deste trabalho foi desenvolver uma ferramenta de classificação automática de bovinos por intermédio de uma Rede Neural Artificial (RNA) de três camadas. Essa rede é conhecida como Multilayer Perceptron (MLP), aqui do tipo feed forward (sem realimentação) e com algoritmo de treinamento backpropagation (retropropagação do erro) com treinamento supervisionado. A ideia foi identificar os grupos de abate e os que requerem alimentação mais intensiva, utilizando como variáveis de entrada da rede massa e altura e como variável de saída, o índice de massa corporal (IMC). Os dados utilizados neste trabalho foram obtidos de um rebanho de 147 vacas Nelore, localizadas na cidade de Santa Rita do Pardo - Mato Grosso do Sul (MS). Dos resultados, a rede obteve um excelente desempenho na fase de treinamento (100 amostras), com erro quadrado médio em torno de 10-5. Já na fase do diagnóstico (operação da rede), foi submetida à rede as 47 amostras restantes dos dados de vacas Nelore que não fizeram parte do treinamento da mesma, desses resultados, a rede apresentou em média, um erro em torno de 0,6% em relação à saída desejada (dados normalizados), o que acarretou num erro de 1 amostra das 47 analisadas.

Bullous lupus erythematosus with an erythema gyratum repens-like pattern

Bullous lupus erythematosus is a rare clinical form of lupus. The diagnosis is challenging and involves the exclusion of other subepidermal bullous dermatoses. We present a 21-year-old woman with erythematosus, polycyclic plaques with vesiculobullae along the periphery, creating an erythema gyratum repens-like pattern on acral regions. The cutaneous biopsy, analytical, and autoimmune studies support the diagnosis of systemic lupus erythematosus. Dapsone and glucocorticosteroids were given with prompt resolution of the lesions within two weeks. To our knowledge this is the first case of bullous lupus erythematosus with this atypical acral presentation.