Activated rate-response is associated with increased mortality risk in cardiac device carriers with acute heart failure.

AIMS: This study investigated whether an activated R-mode in patients carrying a cardiac implantable electronic device (CIED) is associated with worse prognosis during and after an episode of acutely decompensated heart failure (AHF). METHODS: Six hundred and twenty-three patients participating in an ongoing prospective cohort study that phenotypes and follows patients admitted for AHF were studied. We compared CIED carriers with activated R-mode stimulation (CIED-R) to CIED carriers not in R-mode (CIED-0) and patients without CIEDs (no-CIED). The independent impact of R-mode activation on 12-month all-cause death was examined using uni- and multivariable Cox proportional hazards regression taking into account potential confounders, and hazard ratios (HR) with their 95% confidence intervals (CI) were reported. RESULTS: Mean heart rate on admission was lower in CIED-R (n = 37, 16% women) vs. CIED-0 (n = 64, 23% women) or no-CIED (n = 511, 43% women): 70 bpm vs. 80 bpm or 82 bpm; both p<0.001. In-hospital mortality was similar across groups, but age- and sex-adjusted all-cause 12-month mortality risk was differentially affected by R-mode activation; CIED-R vs. CIED-0: HR 2.44, 95%CI 1.25-4.74; CIED-R vs. no-CIED: HR 2.61, 95%CI 1.59-4.29. These effects persisted after multivariable adjustment for potential confounders. Within CIED-R, mortality risk was similar in patients with pacemakers vs. ICDs and in subgroups with left ventricular ejection fraction (LVEF) <50% vs. ≥50%. CONCLUSION: In patients admitted with AHF, R-mode stimulation was associated with a significantly increased 12-month mortality risk. Our findings shed new light on "admission heart rate" as a potentially treatable target in AHF. Our data are compatible with the concept that chronotropic incompetence contributes to an adverse outcome in these patients and may not be adequately treated through accelerometer-based R-mode stimulation.

SHIFTR enables the unbiased identification of proteins bound to specific RNA regions in live cells.

RNA-protein interactions determine the cellular fate of RNA and are central to regulating gene expression outcomes in health and disease. To date, no method exists that is able to identify proteins that interact with specific regions within endogenous RNAs in live cells. Here, we develop SHIFTR (Selective RNase H-mediated interactome framing for target RNA regions), an efficient and scalable approach to identify proteins bound to selected regions within endogenous RNAs using mass spectrometry. Compared to state-of-the-art techniques, SHIFTR is superior in accuracy, captures minimal background interactions and requires orders of magnitude lower input material. We establish SHIFTR workflows for targeting RNA classes of different length and abundance, including short and long non-coding RNAs, as well as mRNAs and demonstrate that SHIFTR is compatible with sequentially mapping interactomes for multiple target RNAs in a single experiment. Using SHIFTR, we comprehensively identify interactions of cis-regulatory elements located at the 5' and 3'-terminal regions of authentic SARS-CoV-2 RNAs in infected cells and accurately recover known and novel interactions linked to the function of these viral RNA elements. SHIFTR enables the systematic mapping of region-resolved RNA interactomes for any RNA in any cell type and has the potential to revolutionize our understanding of transcriptomes and their regulation.

SND1 binds SARS-CoV-2 negative-sense RNA and promotes viral RNA synthesis through NSP9.

Regulation of viral RNA biogenesis is fundamental to productive SARS-CoV-2 infection. To characterize host RNA-binding proteins (RBPs) involved in this process, we biochemically identified proteins bound to genomic and subgenomic SARS-CoV-2 RNAs. We find that the host protein SND1 binds the 5' end of negative-sense viral RNA and is required for SARS-CoV-2 RNA synthesis. SND1-depleted cells form smaller replication organelles and display diminished virus growth kinetics. We discover that NSP9, a viral RBP and direct SND1 interaction partner, is covalently linked to the 5' ends of positive- and negative-sense RNAs produced during infection. These linkages occur at replication-transcription initiation sites, consistent with NSP9 priming viral RNA synthesis. Mechanistically, SND1 remodels NSP9 occupancy and alters the covalent linkage of NSP9 to initiating nucleotides in viral RNA. Our findings implicate NSP9 in the initiation of SARS-CoV-2 RNA synthesis and unravel an unsuspected role of a cellular protein in orchestrating viral RNA production.

The relationship between mental health, sleep quality and the immunogenicity of COVID-19 vaccinations.

Sleep modulates the immune response, and sleep loss can reduce vaccine immunogenicity; vice versa, immune responses impact sleep. We aimed to investigate the influence of mental health and sleep quality on the immunogenicity of COVID-19 vaccinations and, conversely, of COVID-19 vaccinations on sleep quality. The prospective CoVacSer study monitored mental health, sleep quality and Anti-SARS-CoV-2-Spike IgG titres in a cohort of 1082 healthcare workers from 29 September 2021 to 19 December 2022. Questionnaires and blood samples were collected before, 14 days, and 3 months after the third COVID-19 vaccination, as well as in 154 participants before and 14 days after the fourth COVID-19 vaccination. Healthcare workers with psychiatric disorders had slightly lower Anti-SARS-CoV-2-Spike IgG levels before the third COVID-19 vaccination. However, this effect was mediated by higher median age and body mass index in this subgroup. Antibody titres following the third and fourth COVID-19 vaccinations ("booster vaccinations") were not significantly different between subgroups with and without psychiatric disorders. Sleep quality did not affect the humoral immunogenicity of the COVID-19 vaccinations. Moreover, the COVID-19 vaccinations did not impact self-reported sleep quality. Our data suggest that in a working population neither mental health nor sleep quality relevantly impact the immunogenicity of COVID-19 vaccinations, and that COVID-19 vaccinations do not cause a sustained deterioration of sleep, suggesting that they are not a precipitating factor for insomnia. The findings from this large-scale real-life cohort study will inform clinical practice regarding the recommendation of COVID-19 booster vaccinations for individuals with mental health and sleep problems.

Influencing factors of anti-SARS-CoV-2-spike-IgG antibody titers in healthcare workers: A cross-section study.

Against the background of the current COVID-19 infection dynamics with its rapid spread of SARS-CoV-2 variants of concern (VOC), the immunity and the vaccine prevention of healthcare workers (HCWs) against SARS-CoV-2 continues to be of high importance. This observational cross-section study assesses factors influencing the level of anti-SARS-CoV-2-spike IgG after SARS-CoV-2 infection or vaccination. One thousand seven hundred and fifty HCWs were recruited meeting the following inclusion criteria: age ≥18 years, PCR-confirmed SARS-CoV-2 infection convalescence and/or at least one dose of COVID-19 vaccination. anti-SARS-CoV-2-spike IgG titers were determined by SERION ELISA agile SARS-CoV-2 IgG. Mean anti-SARS-CoV-2-spike IgG levels increased significantly by number of COVID-19 vaccinations (92.2 BAU/ml for single, 140.9 BAU/ml for twice and 1144.3 BAU/ml for threefold vaccination). Hybrid COVID-19 immunized respondents (after infection and vaccination) had significantly higher antibody titers compared with convalescent only HCWs. Anti-SARS-CoV-2-spike IgG titers declined significantly with time after the second vaccination. Smoking and high age were associated with lower titers. Both recovered and vaccinated HCWs presented a predominantly good humoral immune response. Smoking and higher age limited the humoral SARS-CoV-2 immunity, adding to the risk of severe infections within this already health impaired collective.

Virus variant-specific clinical performance of SARS coronavirus two rapid antigen tests in point-of-care use, from November 2020 to January 2022.

OBJECTIVES: Antigen rapid diagnostic tests (RDTs) for SARS coronavirus 2 (SARS-CoV-2) are quick, widely available, and inexpensive. Consequently, RDTs have been established as an alternative and additional diagnostic strategy to quantitative reverse transcription polymerase chain reaction (RT-qPCR). However, reliable clinical and large-scale performance data specific to a SARS-CoV-2 virus variant of concern (VOC) are limited, especially for the Omicron VOC. The aim of this study was to compare RDT performance among different VOCs. METHODS: This single-centre prospective performance assessment compared RDTs from three manufacturers (NADAL, Panbio, MEDsan) with RT-qPCR including deduced standardized viral load from oropharyngeal swabs for detection of SARS-CoV-2 in a clinical point-of-care setting from November 2020 to January 2022. RESULTS: Among 35 479 RDT/RT-qPCR tandems taken from 26 940 individuals, 164 of the 426 SARS-CoV-2 positive samples tested true positive with an RDT corresponding to an RDT sensitivity of 38.50% (95% CI, 34.00-43.20%), with an overall specificity of 99.67% (95% CI, 99.60-99.72%). RDT sensitivity depended on viral load, with decreasing sensitivity accompanied by descending viral load. VOC-dependent sensitivity assessment showed a sensitivity of 42.86% (95% CI, 32.82-53.52%) for the wild-type SARS-CoV-2, 43.42% (95% CI, 32.86-54.61%) for the Alpha VOC, 37.67% (95% CI, 30.22-45.75%) for the Delta VOC, and 33.67% (95% CI, 25.09-43.49%) for the Omicron VOC. Sensitivity in samples with high viral loads of ≥106 SARS-CoV-2 RNA copies per mL was significantly lower in the Omicron VOC (50.00%; 95% CI, 36.12-63.88%) than in the wild-type SARS-CoV-2 (79.31%; 95% CI, 61.61-90.15%; p 0.015). DISCUSSION: RDT sensitivity for detection of the Omicron VOC is reduced in individuals infected with a high viral load, which curtails the effectiveness of RDTs. This aspect furthert: limits the use of RDTs, although RDTs are still an irreplaceable diagnostic tool for rapid, economic point-of-care and extensive SARS-CoV-2 screening.

Impact of coronavirus disease (COVID-19) pandemic on physical activity of patients with cardiac implantable electronic devices-A remote monitoring study.

OBJECTIVES: The study aims to investigate the impact of COVID-19 pandemic on physical activity and frequency of implantable cardioverter-defibrillator (ICD) therapies of patients with cardiac implantable electronic devices. METHODS AND RESULTS: Physical activity, heart rate and ICD-therapies were assessed via routine remote monitoring over two years. We focussed on a 338-day period during COVID-19 pandemic that was divided in 6 time-intervals defined by public health interventions and compared to the previous regular year. Paired nonparametric longitudinal analysis was performed to detect differences between time-intervals. To model effects of age, sex and time we applied a nonparametric ANOVA-type-statistic. 147 patients with cardiac implantable electronic devices were analysed. Longitudinal analysis of physical activity in 2019 and 2020 showed a specific weekly and seasonal pattern. Physical activity was reduced during the pandemic (mean daily physical activity 2019: 12.4% vs. 2020: 11.5%; p<0.0001) with the strongest reductions (fold changes 0.885/0.889, p<0.0001/p<0.0001) during the two lockdown-periods. In older patients (>70 years), physical activity was decreased in every time-interval of the year 2020. In time-intervals of eased restrictions, physical activity of younger patients (≤70 years) was not different compared to 2019. No variation in mean heart rate, arrhythmia-burden and count of ICD-therapies was found. CONCLUSION: Physical activity shows fluctuations dependent on days of the week and time of the year. During the pandemic, physical activity was reduced in patients with cardiac implantable electronic devices with the strongest reductions during lockdown-periods. Younger patients resumed former levels of physical activity in times of eased restrictions while older patients remained less active. Thus, activation of the elderly population is important to prevent long-term health impairments due to the pandemic.

Errorless learning and assistive technology did not improve the negative prognosis for severe dressing impairment after stroke if persisting for two weeks: A randomized controlled trial.

Following severe cerebrovascular accidents, patients are often unable to dress themselves. Little is known about the persistence and treatment of this impairment. Study 1 followed 23 patients who were (1) completely dependent on others for help with dressing (2) for two weeks continually until their discharge from the rehabilitation unit. Study 2, a randomized controlled trial of 24 patients, examined the effects of errorless learning and RehaGoal App-based dressing practice on recovery in dressing ability-impaired patients who also experienced visuospatial neglect and/or apraxia. The control and intervention groups both underwent a standard therapy in the rehab unit; the intervention group additionally received dressing training (seven sessions of 45 min). The primary outcome measure was the score on an adapted version of the Nottingham Stroke Dressing Assessment; secondary outcome measures were the Barthel Index and Functional Independence Measure. Less than one-third of the patients in Study1, showed improvement. In Study 2, the intervention produced no specific effect on patients' dressing ability. However, apraxia and neglect predicted improvement for both groups. If patients depend completely on assistance for dressing for two weeks, prospects for recovery are limited. Future studies should include additional intervention sessions and incorporate treatments for neglect or apraxia.

Guiding patients with traumatic brain injury through the instrumental activities of daily living with the RehaGoal App: a feasibility study.

PURPOSE: Individuals with traumatic brain injuries (TBI) often experience executive function impairments that impact activities of daily living. Assistive technologies can help overcome these disabilities and Goal Management Training (GMT) provides an effective therapeutic approach for treating such impairments. To capture the benefits of GMT with assistive technology we developed the RehaGoal App. In this study, we investigate whether combining a modified GMT (mGMT) with the RehaGoal App is feasible in terms of study design, and preliminary evaluation of the attainment of self-defined goals. We also examine if the app produces useful metrics data, tests its usability, and gauges its potential for improving goal attainment. METHODS: We used a case study design to evaluate four individuals with impairments in executive functions after TBI. They underwent an 8-week mGMT and RehaGoal App intervention to achieve a self-defined goal. To investigate the intervention's feasibility, we collected Goal Attainment Scale (GAS) scores at two-time points, neuropsychological data at study start, System Usability Scale (SUS) scores at study end, and metrics data throughout the study period. RESULTS: Participant retention and compliance rates were high. All participants improved on GAS. Metrics data was collected successfully and revealed different participant usage behaviours. Overall, the SUS scores of the participants indicated excellent app usability. CONCLUSIONS: The intervention was feasible but the study design should be modified. Preliminary evaluation of GAS, SUS, and metrics data provided useful insights on user behaviour, app usability, and its role in achieving self-defined goals. The app received overall positive participant ratings.IMPLICATION FOR REHABILITATIONMetric data can be useful as it can give therapists additional opportunities to gain more information about the realization of intervention tasks between the therapy sessions allowing them to use this information to adjust therapy elements.RehaGoal App in combination with a modified GMT may be able to support participants with impairment in executive functions in completing the task of daily living.The study shows that the RehaGoal App is feasible in rehabilitation for a small sample size and that it may be scaled up in the future larger randomized controlled trial.

Selective egg cell polyspermy bypasses the triploid block.

Polyploidization, the increase in genome copies, is considered a major driving force for speciation. We have recently provided the first direct in planta evidence for polyspermy induced polyploidization. Capitalizing on a novel sco1-based polyspermy assay, we here show that polyspermy can selectively polyploidize the egg cell, while rendering the genome size of the ploidy-sensitive central cell unaffected. This unprecedented result indicates that polyspermy can bypass the triploid block, which is an established postzygotic polyploidization barrier. In fact, we here show that most polyspermy-derived seeds are insensitive to the triploid block suppressor admetos. The robustness of polyspermy-derived plants is evidenced by the first transcript profiling of triparental plants and our observation that these idiosyncratic organisms segregate tetraploid offspring within a single generation. Polyspermy-derived triparental plants are thus comparable to triploids recovered from interploidy crosses. Our results expand current polyploidization concepts and have important implications for plant breeding.

Ever since Darwin published his most famous book on the theory of evolution, scientists have sought to identify the mechanisms that drive the formation of new species. This is especially true for plant biologists who have long been fascinated by the extraordinary diversity of flowering plants.Many species of flowering plant first evolved after a dramatic increase in the DNA content of an individual plant, a process termed polyploidization. Most explanations for polyploidization involve a pollen grain making sperm that mistakenly contain two sets of chromosomes rather than one. Yet, it is difficult to reconcile this explanation with an important aspect of plant reproduction ­ the so-called "triploid block".Fertilization in flowering plants is more complicated than in animals. While one sperm fertilizes the egg cell to make the plant embryo, a second sperm from the same pollen grain must fertilize another cell to form the endosperm, the tissue that will nourish the embryo as it develops. This means that sperm with twice the normal number of chromosomes would affect the DNA content of both the embryo and the endosperm. Yet, an endosperm that receives extra paternal DNA typically halts the development of the seed via a process known as the triploid block, meaning it was not clear how often this process would actually result in a polyploid plant.In 2017, researchers reported that plants can, on rare occasions, generate polyploid offspring via a different route: the fertilization of one egg with two sperm rather than one. Now, Mao et al. ­ who include several researchers involved in the 2017 study ­ show that this process, termed "polyspermy", can introduce extra copies of DNA into just the egg cell, meaning it can bypass the triploid block of the endosperm.The experiments involved a model plant called Arabidopsis, and a screen of over 55,000 seeds identified about a dozen with embryos that had three parents, one mother and two fathers. Notably, most of these three-parent embryos developed in seeds that contained endosperm with the regular number of chromosomes and hence escaped the triploid block.These new results show that polyspermy provides plants with a means to essentially sneak extra copies of DNA 'behind the back' of the DNA-sensitive endosperm and into the next generation. They also give new insight in how polyploidization may have shaped the evolution of flowering plants and have important implications for agriculture where the breeding of new "hybrid" crops has often been limited by incompatibilities in the endosperm.

Metabolic footprint and intestinal microbial changes in response to dietary proteins in a pig model.

Epidemiological studies revealed that dietary proteins can contribute to the modulation of the cardiovascular disease risk. Still, direct effects of dietary proteins on serum metabolites and other health-modulating factors have not been fully explored. Here, we compared the effects of dietary lupin protein with the effects of beef protein and casein on the serum metabolite profile, cardiovascular risk markers and the fecal microbiome. Pigs were fed diets containing 15% of the respective proteins for 4 weeks. A classification analysis of the serum metabolites revealed six biomarker sets of two metabolites each that discriminated between the intake of lupin protein, lean beef or casein. These biomarker sets included 1- and 3-methylhistidine, betaine, carnitine, homoarginine and methionine. The study revealed differences in the serum levels of the metabolites 1- and 3- methylhistidine, homoarginine, methionine and homocysteine, which are involved in the one-carbon cycle. However, these changes were not associated with differences in the methylation capacity or the histone methylation pattern. With the exception of serum homocysteine and homoarginine levels, other cardiovascular risk markers, such as the homeostatic model assessment index, trimethylamine-N-oxide and lipids, were not influenced by the dietary protein source. However, the composition of the fecal microorganisms was markedly changed by the dietary protein source. Lupin-protein-fed pigs exhibited more species from the phyla Bacteroidetes and Firmicutes than the other two groups. In conclusion, different dietary protein sources induce distinct serum metabolic fingerprints, have an impact on the cardiovascular risk and modulate the composition of the fecal microbiome.

Age- and Diabetes-Related Changes in the Free Fatty Acid Composition of the Human Stratum Corneum.

Of particular importance for Stratum corneum (SC) lipids are the free fatty acids (FFAs). Age-related changes of the SC structure lead to diminished capacity for barrier compensation. The aims of this cross-sectional study were to identify even-numbered especially odd-numbered FFAs within the intercorneocytic lamellar lipid structures of the SC and to explore age- and diabetes-related changes in FFAs. Gas chromatography - flame ionisation detection was used to qualitatively and quantitatively assess FFAs extracted from the SC. 110 subjects aged over 60 years (elderly/healthy), 110 subjects aged 18-40 (young/healthy) and 38 subjects with diabetes mellitus aged 18-40 (young/diabetic) were investigated. Overall, odd-numbered FFAs comprised about 21, 23 and 24% of total FFAs in subgroups elderly/healthy, young/healthy and young/diabetic. The most abundant short-chain FFAs were C16: 0 and C18: 0 and long-chain FFAs were C24: 0 and C26: 0. Only levels of C15: 0 and C17: 0 decreased with age. In contrast, levels of C18: 2 and C19 were significantly decreased and levels of C15, C17, C18: 1 and C23 were significantly increased in young diabetic subjects. In general, compared with younger healthy subjects, FFA composition was only partly significantly altered in older healthy subjects but was significantly altered in younger diabetic subjects.

Transcriptome dynamics at Arabidopsis graft junctions reveal an intertissue recognition mechanism that activates vascular regeneration.

The ability for cut tissues to join and form a chimeric organism is a remarkable property of many plants; however, grafting is poorly characterized at the molecular level. To better understand this process, we monitored genome-wide gene expression changes in grafted Arabidopsis thaliana hypocotyls. We observed a sequential activation of genes associated with cambium, phloem, and xylem formation. Tissues above and below the graft rapidly developed an asymmetry such that many genes were more highly expressed on one side than on the other. This asymmetry correlated with sugar-responsive genes, and we observed an accumulation of starch above the graft junction. This accumulation decreased along with asymmetry once the sugar-transporting vascular tissues reconnected. Despite the initial starvation response below the graft, many genes associated with vascular formation were rapidly activated in grafted tissues but not in cut and separated tissues, indicating that a recognition mechanism was activated independently of functional vascular connections. Auxin, which is transported cell to cell, had a rapidly elevated response that was symmetric, suggesting that auxin was perceived by the root within hours of tissue attachment to activate the vascular regeneration process. A subset of genes was expressed only in grafted tissues, indicating that wound healing proceeded via different mechanisms depending on the presence or absence of adjoining tissues. Such a recognition process could have broader relevance for tissue regeneration, intertissue communication, and tissue fusion events.

myTAI: evolutionary transcriptomics with R.

Motivation: Next Generation Sequencing (NGS) technologies generate a large amount of high quality transcriptome datasets enabling the investigation of molecular processes on a genomic and metagenomic scale. These transcriptomics studies aim to quantify and compare the molecular phenotypes of the biological processes at hand. Despite the vast increase of available transcriptome datasets, little is known about the evolutionary conservation of those characterized transcriptomes. Results: The myTAI package implements exploratory analysis functions to infer transcriptome conservation patterns in any transcriptome dataset. Comprehensive documentation of myTAI functions and tutorial vignettes provide step-by-step instructions on how to use the package in an exploratory and computationally reproducible manner. Availability and implementation: The open source myTAI package is available at https://github.com/HajkD/myTAI and https://cran.r-project.org/web/packages/myTAI/index.html. Contact: hgd23@cam.ac.uk. Supplementary information: Supplementary data are available at Bioinformatics online.