ProtASR: an evolutionary framework for ancestral protein reconstruction with selection on folding stability

The computational reconstruction of ancestral proteins provides information on past biological events and has practical implications for biomedicine and biotechnology. Currently available tools for ancestral sequence reconstruction (ASR) are often based on empirical amino acid substitution models that assume that all sites evolve at the same rate and under the same process. However, this assumption is frequently violated because protein evolution is highly heterogeneous due to different selective constraints among sites. Here, we present ProtASR, a new evolutionary framework to infer ancestral protein sequences accounting for selection on protein stability. First, ProtASR generates site-specific substitution matrices through the structurally constrained mean-field (MF) substitution model, which considers both unfolding and misfolding stability. We previously showed that MF models outperform empirical amino acid substitution models, as well as other structurally constrained substitution models, both in terms of likelihood and correctly inferring amino acid distributions across sites. In the second step, ProtASR adapts a well-established maximum-likelihood (ML) ASR procedure to infer ancestral proteins under MF models. A known bias of ML ASR methods is that they tend to overestimate the stability of ancestral proteins by underestimating the frequency of deleterious mutations. We compared ProtASR under MF to two empirical substitution models (JTT and CAT), reconstructing the ancestral sequences of simulated proteins. ProtASR yields reconstructed proteins with less biased stabilities, which are significantly closer to those of the simulated proteins. Analysis of extant protein families suggests that folding stability evolves through time across protein families, potentially reflecting neutral fluctuation. Some families exhibit a more constant protein folding stability, while others are more variable. ProtASR is freely available from https://github.com/miguelarenas/protasr and includes detailed documentation and ready-to-use examples. It runs in seconds/minutes depending on protein length and alignment size

Metabolomic serum abnormalities in dogs with hepatopathies

Hepatopathies can cause major metabolic abnormalities in humans and animals. This study examined differences in serum metabolomic parameters and patterns in left-over serum samples from dogs with either congenital portosystemic shunts (cPSS, n = 24) or high serum liver enzyme activities (HLEA, n = 25) compared to control dogs (n = 64). A validated targeted proton nuclear magnetic resonance spectroscopy platform was used to assess 123 parameters. Principal component analysis of the serum metabolome demonstrated distinct clustering among individuals in each group, with the cluster of HLEA being broader compared to the other groups, presumably due to the wider spectrum of hepatic diseases represented in these samples. While younger and older adult control dogs had very similar metabolomic patterns and clusters, there were changes in many metabolites in the hepatopathy groups. Higher phenylalanine and tyrosine concentrations, lower branched-chained amino acids (BCAAs) concentrations, and altered fatty acid parameters were seen in cPSS dogs compared to controls. In contrast, dogs with HLEA had increased concentrations of BCAAs, phenylalanine, and various lipoproteins. Machine learning based solely on the metabolomics data showed excellent group classification, potentially identifying a novel tool to differentiate hepatopathies. The observed changes in metabolic parameters could provide invaluable insight into the pathophysiology, diagnosis, and prognosis of hepatopathies.Peer reviewe

A Remote Patient-Monitoring System for Intensive Care Medicine: Mixed Methods Human-Centered Design and Usability Evaluation

Background: Continuous monitoring of vital signs is critical for ensuring patient safety in intensive care units (ICUs) and is becoming increasingly relevant in general wards. The effectiveness of health information technologies such as patient-monitoring systems is highly determined by usability, the lack of which can ultimately compromise patient safety. Usability problems can be identified and prevented by involving users (ie, clinicians). Objective: In this study, we aim to apply a human-centered design approach to evaluate the usability of a remote patient-monitoring system user interface (UI) in the ICU context and conceptualize and evaluate design changes. Methods: Following institutional review board approval (EA1/031/18), a formative evaluation of the monitoring UI was performed. Simulated use tests with think-aloud protocols were conducted with ICU staff (n=5), and the resulting qualitative data were analyzed using a deductive analytic approach. On the basis of the identified usability problems, we conceptualized informed design changes and applied them to develop an improved prototype of the monitoring UI. Comparing the UIs, we evaluated perceived usability using the System Usability Scale, performance efficiency with the normative path deviation, and effectiveness by measuring the task completion rate (n=5). Measures were tested for statistical significance using a 2-sample t test, Poisson regression with a generalized linear mixed-effects model, and the N-1 chi-square test. P<.05 were considered significant. Results: We found 37 individual usability problems specific to monitoring UI, which could be assigned to six subcodes: usefulness of the system, response time, responsiveness, meaning of labels, function of UI elements, and navigation. Among user ideas and requirements for the UI were high usability, customizability, and the provision of audible alarm notifications. Changes in graphics and design were proposed to allow for better navigation, information retrieval, and spatial orientation. The UI was revised by creating a prototype with a more responsive design and changes regarding labeling and UI elements. Statistical analysis showed that perceived usability improved significantly (System Usability Scale design A: mean 68.5, SD 11.26, n=5; design B: mean 89, SD 4.87, n=5; P=.003), as did performance efficiency (normative path deviation design A: mean 8.8, SD 5.26, n=5; design B: mean 3.2, SD 3.03, n=5; P=.001), and effectiveness (design A: 18 trials, failed 7, 39% times, passed 11, 61% times; design B: 20 trials, failed 0 times, passed 20 times; P=.002). Conclusions: Usability testing with think-aloud protocols led to a patient-monitoring UI with significantly improved usability, performance, and effectiveness. In the ICU work environment, difficult-to-use technology may result in detrimental outcomes for staff and patients. Technical devices should be designed to support efficient and effective work processes. Our results suggest that this can be achieved by applying basic human-centered design methods and principles. Trial Registration: ClinicalTrials.gov NCT03514173; https://clinicaltrials.gov/ct2/show/NCT0351417

Мотивационное управление персоналом на примере компании ООО "Мобител"

Цель дипломной работы: анализ системы мотивационного управления в организации и разработка направлений его совершенствования. В ходе работы проводились практические исследования персонала, выявлялся мотивационный тип, определялась степень информативности персонала организации о системе мотивации (мотивационная среда). Был проведен практический анализ соотношения типов мотивации с формами. В ходе исследования применялось несколько практических методик по формированию мотивационной программы в компании. Степень внедрения: ряд рекомендаций по совершенствованию мотивационного управления персоналом были внедрены в практику управления ООО "Мобител".The purpose of the thesis: analysis of the system of motivational management in the organization and development of directions for its improvement. In the course of the work, practical research of personnel was carried out, the motivational type was revealed, the degree of information of the personnel of the organization about the system of motivation (motivational environment) was determined. A practical analysis of the relationship between types of motivation and forms was carried out. In the course of the research, several practical methods were used to form a motivational program in the company. Degree of implementation: a number of recommendations for improving motivational management of personnel were introduced into the practice of the management of LLC "Mobitel"

The role of cell-free hemoglobin and haptoglobin in acute kidney injury in critically ill adults with ARDS and therapy with VV ECMO

Background: Increased plasma concentrations of circulating cell-free hemoglobin (CFH) are supposed to contribute to the multifactorial etiology of acute kidney injury (AKI) in critically ill patients while the CFH-scavenger haptoglobin might play a protective role. We evaluated the association of CFH and haptoglobin with AKI in patients with an acute respiratory distress syndrome (ARDS) requiring therapy with VV ECMO. Methods: Patients with CFH and haptoglobin measurements before initiation of ECMO therapy were identified from a cohort of 1044 ARDS patients and grouped into three CFH concentration groups using a risk stratification. The primary objective was to assess the association of CFH and haptoglobin with KDIGO stage 3 AKI. Further objectives included the identification of a target haptoglobin concentration to protect from CFH-associated AKI. Measurements and main results: Two hundred seventy-three patients fulfilled the inclusion criteria. Of those, 154 patients (56.4%) had AKI at ECMO initiation. The incidence of AKI increased stepwise with increasing concentrations of CFH reaching a plateau at 15 mg/dl. Compared to patients with low [= 15 mg/dl] CFH concentrations had a three- and five-fold increased risk for AKI (adjusted odds ratio [OR] moderate vs. low, 2.69 [95% CI, 1.25-5.95], P = 0.012; and OR high vs. low, 5.47 [2.00-15.9], P = 0.001). Among patients with increased CFH concentrations, haptoglobin plasma levels were lower in patients with AKI compared to patients without AKI. A haptoglobin concentration greater than 2.7 g/l in the moderate and 2.4 g/l in the high CFH group was identified as clinical cutoff value to protect from CFH-associated AKI (sensitivity 89.5% [95% CI, 83-96] and 90.2% [80-97], respectively). Conclusions: In critically ill patients with ARDS requiring therapy with VV ECMO, an increased plasma concentration of CFH was identified as independent risk factor for AKI. Among patients with increased CFH concentrations, higher plasma haptoglobin concentrations might protect from CFH-associated AKI and should be subject of future research

Optogenetic Peripheral Nerve Immunogenicity

Optogenetic technologies have been the subject of great excitement within the scientific community for their ability to demystify complex neurophysiological pathways in the central (CNS) and peripheral nervous systems (PNS). The excitement surrounding optogenetics has also extended to the clinic with a trial for ChR2 in the treatment of retinitis pigmentosa currently underway and additional trials anticipated for the near future. In this work, we identify the cause of loss-of-expression in response to transdermal illumination of an optogenetically active peroneal nerve following an anterior compartment (AC) injection of AAV6-hSyn-ChR2(H134R) with and without a fluorescent reporter. Using Sprague Dawley Rag2−/− rats and appropriate controls, we discover optogenetic loss-of-expression is chiefly elicited by ChR2-mediated immunogenicity in the spinal cord, resulting in both CNS motor neuron death and ipsilateral muscle atrophy in both low and high Adeno-Associated Virus (AAV) dosages. We further employ pharmacological immunosuppression using a slow-release tacrolimus pellet to demonstrate sustained transdermal optogenetic expression up to 12 weeks. These results suggest that all dosages of AAV-mediated optogenetic expression within the PNS may be unsafe. Clinical optogenetics for both PNS and CNS applications should take extreme caution when employing opsins to treat disease and may require concurrent immunosuppression. Future work in optogenetics should focus on designing opsins with lesser immunogenicity.MIT Media Lab Consortiu

Impact of selected baking and vacuum cooling parameters on the quality of toast bread

Erworben im Rahmen der Schweizer Nationallizenzen (http://www.nationallizenzen.ch)​Vacuum cooling of baked goods can deliver many advantages in terms of product quality and productivity, such as higher volumes and shorter cooling times. However, the associated high costs and the need to adjust baking protocols are of relevance and more information is needed. This paper examines the influence of two main baking protocol parameters on the quality of toast bread, i.e. oven temperature and baking time reduction. Resulting toast bread characteristics including specific bread volume, concavity, browning index, crust and crumb hardness and aw-value were analysed as well as process-dependent core temperature and water loss. In order to compensate for water loss during vacuum cooling and still achieve optimal toast bread quality, a final bread core temperature of 98 °C at the end of baking gave best results, regardless of oven temperature. It was further shown that cooling time can be reduced by a factor of 10 if the baking protocol is optimally adjusted, hinting at a huge potential to increase productivity for industrial applications. In summary, it can be stated that vacuum cooling requires a tailored reduction in baking time in order to compensate for water loss from vacuum cooling while retaining sufficient structural cohesion to resist deformation of the bread

Children and older adults exhibit distinct sub-optimal cost-benefit functions when preparing to move their eyes and hands

"© 2015 Gonzalez et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited"Numerous activities require an individual to respond quickly to the correct stimulus. The provision of advance information allows response priming but heightened responses can cause errors (responding too early or reacting to the wrong stimulus). Thus, a balance is required between the online cognitive mechanisms (inhibitory and anticipatory) used to prepare and execute a motor response at the appropriate time. We investigated the use of advance information in 71 participants across four different age groups: (i) children, (ii) young adults, (iii) middle-aged adults, and (iv) older adults. We implemented 'cued' and 'non-cued' conditions to assess age-related changes in saccadic and touch responses to targets in three movement conditions: (a) Eyes only; (b) Hands only; (c) Eyes and Hand. Children made less saccade errors compared to young adults, but they also exhibited longer response times in cued versus non-cued conditions. In contrast, older adults showed faster responses in cued conditions but exhibited more errors. The results indicate that young adults (18 -25 years) achieve an optimal balance between anticipation and execution. In contrast, children show benefits (few errors) and costs (slow responses) of good inhibition when preparing a motor response based on advance information; whilst older adults show the benefits and costs associated with a prospective response strategy (i.e., good anticipation)

Speaker identification in courtroom contexts - Part I: Individual listeners compared to forensic voice comparison based on automatic-speaker-recognition technology

Expert testimony is only admissible in common law if it will potentially assist the trier of fact to make a decision that they would not be able to make unaided. The present paper addresses the question of whether speaker identification by an individual lay listener (such as a judge) would be more or less accurate than the output of a forensic-voice-comparison system that is based on state-of-the-art automatic-speaker-recognition technology. Listeners listen to and make probabilistic judgements on pairs of recordings reflecting the conditions of the questioned- and known-speaker recordings in an actual case. Reflecting different courtroom contexts, listeners with different language backgrounds are tested: Some are familiar with the language and accent spoken, some are familiar with the language but less familiar with the accent, and others are less familiar with the language. Also reflecting different courtroom contexts: In one condition listeners make judgements based only on listening, and in another condition listeners make judgements based on both listening to the recordings and considering the likelihood-ratio values output by the forensic-voice-comparison system. [Abstract copyright: Copyright © 2022 The Author(s). Published by Elsevier B.V. All rights reserved.