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

Intronic AT skew is a defendable proxy for germline transcription but does not predict crossing-over or protein evolution rates in Drosophila melanogaster

Recent evidence suggests that germline transcription may affect both protein evolutionary rates, possibly mediated by repair processes, and recombination rates, possibly mediated by chromatin and epigenetic modification. Here, we test these propositions in Drosophila melanogaster. The challenge for such analyses is to provide defendable measures of germline gene expression. Intronic AT skew is a good candidate measure as it is thought to be a consequence, at least in part, of transcription-coupled repair. Prior evidence suggests that intronic AT skew in D. melanogaster is not affected by proximity to intron extremities and differs between transcribed DNA and flanking sequence. We now also establish that intronic AT skew is a defendable proxy for germline expression as (a) it is more similar than expected by chance between introns of the same gene (which is not accounted for by physical proximity), (b) is correlated with male germline expression, and (c) is more pronounced in broadly expressed genes. Furthermore, (d) a trend for intronic skew to differ between 3' and 5' ends of genes is particular to broadly expressed genes. Finally, (e) controlling for physical distance, introns of proximate genes are most different in skew if they have different tissue specificity. We find that intronic AT skew, employed as a proxy for germline transcription, correlates neither with recombination rates nor with the rate of protein evolution. We conclude that there is no prima facie evidence that germline expression modulates recombination rates or monotonically affects protein evolution rates in D. melanogaster

The relationship between hospital patients' ratings of quality of care and communication

Objective To assess the relationship between hospital patients' quality of care ratings and their experiences with health-related information exchanges and communication during hospitalization. Design Cross-sectional multivariate dimensional analysis of data from a quality of care experience questionnaire of hospital patients comparing scores across three levels of reported satisfaction. Setting and participants Five thousand nine hundred and fifty-two patients from a Swiss University Hospital responded to the questionnaire at discharge during 2010. Main outcome measures Survey questions measuring patients' evaluation of quality of care, patient loyalty and overall satisfaction. Results Different levels of reported satisfaction are associated with differing experiences of health-related information and communication during a hospital stay. Conclusions Patients who report lower satisfaction appear to attribute to the hospital staff enduring negative dispositions from behaviours that may be due to specific situational contexts. Negative experiences appear to influence scores on most other communication and information domains. Patients who report higher satisfaction, in contrast, appear to differentiate negative experiences and positive experiences and they appear to relativize and compartmentalize negative experiences associated with their hospital sta

Association between potassium concentrations, variability and supplementation, and in‑hospital mortality in ICU patients: a retrospective analysis

BACKGROUND: Serum potassium concentrations are commonly between 3.5 and 5.0 mmol/l. Standardised protocols for potassium range and supplementation in the ICU are lacking. The purpose of this retrospective analysis of ICU patients was to investigate potassium concentrations, variability and supplementation, and their association with in-hospital mortality. METHODS: ICU patients ≥ 18 years, with ≥ 2 serum potassium values, treated at the Charité - Universitätsmedizin Berlin between 2006 and 2018 were eligible for inclusion. We categorised into groups of mean potassium concentrations:  3.5-4.0, > 4.0-4.5, > 4.5-5.0, > 5.0-5.5, > 5.5 mmol/l and potassium variability: 1st, 2nd and ≥ 3rd standard deviation (SD). We analysed the association between the particular groups and in-hospital mortality and performed binary logistic regression analysis. Survival curves were performed according to Kaplan-Meier and tested by Log-Rank. In a subanalysis, the association between potassium supplementation and in-hospital mortality was investigated. RESULTS: In 53,248 ICU patients with 1,337,742 potassium values, the lowest mortality (3.7%) was observed in patients with mean potassium concentrations between > 3.5 and 4.0 mmol/l and a low potassium variability within the 1st SD. Binary logistic regression confirmed these results. In a subanalysis of 22,406 ICU patients (ICU admission: 2013-2018), 12,892 (57.5%) received oral and/or intravenous potassium supplementation. Potassium supplementation was associated with an increase in in-hospital mortality in potassium categories from > 3.5 to 4.5 mmol/l and in the 1st, 2nd and ≥ 3rd SD (p < 0.001 each). CONCLUSIONS: ICU patients may benefit from a target range between 3.5 and 4.0 mmol/l and a minimal potassium variability. Clear potassium target ranges have to be determined. Criteria for widely applied potassium supplementation should be critically discussed. Trial registration German Clinical Trials Register, DRKS00016411. Retrospectively registered 11 January 2019, http://www.drks.de/DRKS00016411

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