Charting and tracking the evolution of the SARS CoV-2 coronavirus variants of concern with protein mass spectrometry.

The evolution of the SARS-CoV2 coronavirus spike S-protein is studied using a mass spectrometry based protein phylogenetic approach. A study of a large dataset comprising sets of peptide masses derived from over 3000 proteins of the SARS-CoV2 virus shows that the approach is capable of resolving and correctly displaying the evolution of the major variants of concern. Using these numerical datasets, through a pairwise comparison of sets of proteolytic peptide masses for each protein, the tree is built without the need for the sequence data itself or any sequence alignment. In the same analysis, single point mutations are calculated from peptide mass differences of different protein sets and these are displayed at the branch nodes on the tree. The tree topology is found to be consistent with that generated using conventional sequence-based phylogenetics by a manual visualisation and using a tree comparison algorithm. The mass tree resolves major variants of the virus and displays non-synonymous mutations, calculated based on the mass data alone, on the tree that enable protein evolution to be charted and tracked along interconnected branches. Tracking the evolution of the SARS-CoV2 coronavirus S-protein is of particular importance given its role in the attachment of the virus to host cells ahead of viral replication.

Detection of SARS CoV-2 coronavirus omicron variant with mass spectrometry.

Mass mapping using high resolution mass spectrometry has been applied to identify and rapidly distinguish the omicron variant of the SARS-CoV2 coronavirus strains from other major variants of concern. Insertions, deletions and mutations within the surface spike protein result in associated mass differences in the mass maps that distinguish the variant from the originating strain and the preceding alpha, beta, gamma and delta variants of concern. The same mass map profiles can also be used to construct phylogenetic trees, without the need for protein (or gene) sequences or their alignment, in order to chart and study the origins of the variants, or any other strains. The speed and sensitivity of mass spectrometric analysis is demonstrated for a preliminary set of clinical specimens with comparable sample handling to that required in PCR based approaches.

Analysis of bacterial biotyping datasets with a mass-based phylonumerics approach.

A mass tree, phylonumerics approach, is implemented for the first time with expressed protein mass data acquired in biotyping applications. It is shown, for two separate and diverse bacterial datasets, that the MassTree algorithm can be used to build phylogenetic trees in a single step that mirror those output by biotyping analysis software in the form of a main spectral profile (MSP) dendrogram or alike. Adapted for these applications to accommodate higher mass inputs and large mass error tolerances for pairwise matching, the mass tree algorithm and approach offers an alternative to commercial biotyping platforms by utilizing datasets acquired from any mass spectrometer without the need for specialized and expensive software.

Detection and evolution of SARS-CoV-2 coronavirus variants of concern with mass spectrometry.

Mass mapping using high-resolution mass spectrometry has been applied to identify and rapidly distinguish SARS-CoV-2 coronavirus strains across five major variants of concern. Deletions or mutations within the surface spike protein across these variants, which originated in the UK, South Africa, Brazil and India (known as the alpha, beta, gamma and delta variants respectively), lead to associated mass differences in the mass maps. Peptides of unique mass have thus been determined that can be used to identify and distinguish the variants. The same mass map profiles are also utilized to construct phylogenetic trees, without the need for protein (or gene) sequences or their alignment, in order to chart and study viral evolution. The combined strategy offers advantages over conventional PCR-based gene-based approaches exploiting the ease with which protein mass maps can be generated and the speed and sensitivity of mass spectrometric analysis.

Epinephrine at 25°C Core Body Temperature and During Rewarming: Case Report of Successful Infant Resuscitation After Cold Water Submersion.

Epinephrine plays a controversial role in accidental hypothermia (<30°C). We report its use in the advanced life support of a 13-month-old white girl with pulseless electrical activity and 25°C core body temperature after 32 minutes of submersion in a fast-running Swiss mountain stream at 8°C. Two doses of epinephrine (10 µg/kg) were given in the field, followed by 12 doses (10 µg/kg) and an infusion of 0.1 µg/kg per minute during rewarming. Spontaneous circulation returned at 29.5°C after 2.5 hours of cardiopulmonary resuscitation. Neurologic long-term outcome was excellent. We conclude that in the presence of nonshockable rhythm the benefits of epinephrine may outweigh the risks of side effects when used in pediatric advanced life support for accidental hypothermia.

Reduction of SR Ca2+ leak and arrhythmogenic cellular correlates by SMP-114, a novel CaMKII inhibitor with oral bioavailability.

Sarcoplasmic reticulum (SR) Ca2+ leak induced by Ca2+/calmodulin-dependent protein kinase II (CaMKII) is centrally involved in atrial and ventricular arrhythmogenesis as well as heart failure remodeling. Consequently, treating SR Ca2+ leak has been proposed as a novel therapeutic paradigm, but compounds for use in humans are lacking. SMP-114 ("Rimacalib") is a novel, orally available CaMKII inhibitor developed for human use that has already entered clinical phase II trials to treat rheumatoid arthritis. We speculated that SMP-114 might also be useful to treat cardiac SR Ca2+ leak. SMP-114 significantly reduces SR Ca2+ leak (as assessed by Ca2+ sparks) in human atrial (0.72 ± 0.33 sparks/100 µm/s vs. control 3.02 ± 0.91 sparks/100 µm/s) and failing left ventricular (0.78 ± 0.23 vs. 1.69 ± 0.27 sparks/100 µm/s) as well as in murine ventricular cardiomyocytes (0.30 ± 0.07 vs. 1.50 ± 0.28 sparks/100 µm/s). Associated with lower SR Ca2+ leak, we found that SMP-114 suppressed the occurrence of spontaneous arrhythmogenic spontaneous Ca2+ release (0.356 ± 0.109 vs. 0.927 ± 0.216 events per 30 s stimulation cessation). In consequence, post-rest potentiation of Ca2+-transient amplitude (measured using Fura-2) during the 30 s pause was improved by SMP-114 (52 ± 5 vs. 37 ± 4%). Noteworthy, SMP-114 has these beneficial effects without negatively impairing global excitation-contraction coupling: neither systolic Ca2+ release nor single cell contractility was compromised, and also SR Ca2+ reuptake, in line with resulting cardiomyocyte relaxation, was not impaired by SMP-114 in our assays. SMP-114 demonstrated potential to treat SR Ca2+ leak and consequently proarrhythmogenic events in rodent as well as in human atrial cardiomyocytes and cardiomyocytes from patients with heart failure. Further research is necessary towards clinical use in cardiac disease.

Efficacy and NSAID-sparing effect of secukinumab 150 mg in ankylosing spondylitis: results from phase IV ASTRUM study.

Background: Radiographic axial spondyloarthritis (r-axSpA), formerly known as ankylosing spondylitis (AS), is a chronic, inflammatory rheumatic disease associated with symptoms such as inflammatory back pain, morning stiffness, and arthritis. First-line recommendations for patients with AS include treatment with nonsteroidal anti-inflammatory drugs (NSAIDs) for reducing pain and stiffness. Objectives: The objective of our study is to evaluate the efficacy and short-term NSAID-sparing effect of secukinumab in patients with AS currently treated with NSAIDs. Design: We assessed the clinical Assessment of SpondyloArthritis International Society (ASAS20) response to secukinumab and evaluated the extent to which the use of concomitant NSAID can be reduced between weeks 4 and 12 in r-axSpA patients treated with secukinumab 150 mg compared with placebo. Methods: ASTRUM was a prospective 24-week randomized controlled trial of adult patients with active r-axSpA [Bath Ankylosing Spondylitis Disease Activity Index (BASDAI) ⩾4] who had a documented inadequate response to ⩾2 NSAIDs. Patients were randomized (1:1:1) to initiate treatment with subcutaneous secukinumab 150 mg from either week 0 (group 1), week 4 (group 2), or week 16 (group 3). From week 4 onward, tapering of NSAIDs was allowed in all groups. Results: This study included 211 patients (n = 71, 70, and 70 in groups 1, 2, and 3, respectively). ASAS20 response at week 12 for pooled groups 1 and 2 versus group 3 was 51.1% versus 44.3% (p = 0.35). A higher proportion of patients in groups 1 and 2 achieved ASAS40 and BASDAI50 and showed improvements in other secondary clinical outcomes as compared to group 3 at week 16. More patients in groups 1 and 2 versus group 3 stopped their NSAID intake from baseline through week 16. Conclusion: Treatment with secukinumab improved clinical outcomes and showed a short-term NSAID-sparing effect in patients with r-axSpA, even though the primary endpoint was not met. Trial registration: ClinicalTrials.gov; NCT02763046, EudraCT 2015-004575-74.

Acid-base parameters for predicting magnetic resonance imaging measures of neurologic outcome after perinatal hypoxia-ischemia: is the strong ion gap superior to base excess and lactate?

We conducted this study to compare the strong ion gap (SIG) with base excess (BE) and lactate for predicting neurologic outcome measured by magnetic resonance imaging (MRI) in newborns with hypoxic-ischemic encephalopathy (HIE). In a retrospective cohort of 39 newborns with HIE treated with whole-body surface cooling (n = 17) and no cooling (n = 22), we measured blood SIG, BE, and lactate at 4, 24, and 48 hours after birth, and determined cerebral injury severity by T1-, T2-, and diffusion-weighted MRI scores at age 5 days. Lower SIG levels correlated with better neurologic outcome. The highest correlation coefficient (0.63) was in the "no cooling" subcohort between diffusion-weighted scores and SIG levels at 24 hours; the latter also had the highest area under the receiver operating characteristic curve (AUC), 0.90, with positive and negative predictive values of 84 and 90%. SIG outperformed lactate in the "no cooling" subcohort, and vice-versa in the "cooling" subcohort. All BE AUCs were <0.6. Overall, the SIG is similar to lactate as a prognostic parameter. BE levels at 4, 24, and 48 hours after birth do not predict neurologic outcome. While not displacing lactate the SIG is an additional prognostic parameter for newborns in the first 2 days after hypoxia-ischemia.

Interseasonal RSV infections in Switzerland - rapid establishment of a clinician-led national reporting system (RSV EpiCH).

In anticipation of an interseasonal respiratory syncytial virus (RSV) epidemic, a clinician-led reporting system was rapidly established to capture RSV infections in Swiss hospitals, starting in January 2021. Here, we present details of the reporting system and first results to June 2021. An unusual epidemiology was observed with an interseasonal surge of RSV infections associated with COVID-19-related non-pharmacological interventions. These data allowed real-time adjustment of RSV prophylaxis guidelines and consequently underscore the need for and continuation of systematic nationwide RSV surveillance.

Impact of normal saline infusion on postoperative metabolic acidosis.

BACKGROUND: Standard base excess (SBE) is an important parameter for guiding fluid management in postoperative metabolic acidosis. However, individual SBE components, notably the chloride effect (Cl(eff)), provide valuable additional information. Cl(eff) is the deviation of the strong ion difference (SID) from normal caused by chloride loss or increase and represents the effect on SBE of an abnormal chloride-sodium ratio. Many centers use normal saline (NS) for intravascular volume therapy. In this study, we examined the impact of NS infusion on SBE and its chloride-driven component (Cl(eff)) in postoperative children. METHODS: The study was conducted in 119 children who underwent post-heart surgery in a Swiss pediatric intensive care unit. The 72-h postoperative course was divided into six observation periods, during which NS input and its impact on SBE and Cl(eff) were measured per period in each patient, and the results compared between patients infused and not infused with NS during each period. RESULTS: Normal saline was infused in 168/625 observation periods if indicated by volume deficit. Postoperative metabolic acidosis and the acidifying Cl(eff) were aggravated in the first 12 postoperative hours. Over the 72 h, NS infusion simultaneously lowered SBE by -0.06 mm x ml(-1) x kg(-1) body weight infused and Cl(eff) by -0.07 mm. CONCLUSIONS: Implementing serial Cl(eff) assessment could improve postoperative management by disclosing or excluding hyperchloremia as a cause of acidosis undetectable from SBE alone. Calculating the chloride-driven acidifying side effect of NS infusion using Cl(eff) improves the interpretation of SBE values and can optimize fluid management in postoperative metabolic acidosis.

Resin characterization by electro-acoustic measurements.

The electro-acoustic effects, namely the ion vibration potential (IVP) and the colloidal vibration current (CVI), colloidal vibration potential (CVP) first described by P. Debye [P. Debye, J. Chem. Phys. 1 (1933) 13], are a result of charge separation of bound or free ions at different degrees by ultrasonic waves. Today commercial instruments are available to investigate liquid homogeneous and heterogeneous systems. In the present paper the application of this technique for the characterization of salts, protein solutions and resins for biochromatography is shown and valuable information about resins can be derived in a short time. Various resins were investigated with the following results: (1) the CVI magnitude is dependent of several parameters (such as particle size distribution, volume fraction, density difference); (2) the CVI is influenced by the surface modification of the resins. Polymeric modifications decrease the value of CVI. The CVI is generally lower for high capacity resins; (3) the measurement of the electro-acoustic effects can be used to detect small changes in resins. The CVI is dependent of the amount of adsorbed protein in "native" and denatured state.

Intensity noise properties of quantum cascade lasers.

We present investigations of the the relative intensity noise (RIN) of a quantum cascade laser (QC) laser in continuous wave operation. We analyze the intensity noise properties in terms of the relative intensity noise (RIN). In contrast to conventional interband semiconductor diode lasers we obtain a different scaling behavior of RIN with increasing optical output power for QC lasers. From a semiclassical noise model we find that this result is due to the cascaded active regions each incorporating three laser levels, and is therefore a particular feature of QC lasers.

The elastin gene is disrupted in a family with a balanced translocation t(7;16)(q11.23;q13) associated with a variable expression of the Williams-Beuren syndrome.

The Williams-Beuren syndrome (WBS) is a complex developmental disorder with multisystemic manifestations including supravalvular aortic stenosis (SVAS), a so-called elfin face, a hoarse voice, and a specific cognitive phenotype. Most WBS patients have a >1 Mb deletion on one of their chromosomes 7 in q11 but except for elastin, whose haploinsufficiency causes the cardiovascular malformations, it is unknown which genes in the deletion area contribute to the phenotype. We have investigated a family with a cytogenetically balanced translocation t(7;16)(q11.23;q13) in which affected individuals manifested a broad spectrum of clinical phenotypes ranging from a hoarse voice as the only feature to the full WBS phenotype. Molecular cytogenetic and DNA sequence analyses of the translocation breakpoint showed that the cytogenetic rearrangement disrupts the elastin gene locus within intron 5 in the exact same manner in all translocation carriers. The recently described large inversion of the 7q11.23 region was not present in this family. Our data demonstrate that disruption of the elastin gene by a translocation breakpoint may cause classical WBS, atypical WBS, SVAS, or no recognisable phenotype, and provide a clear example for extensive phenotypic variability associated with a position effect in humans.

Comprehensive Geriatric Assessment (CGA) in general practice: results from a pilot study in Vorarlberg, Austria.

BACKGROUND: Most comprehensive geriatric assessment (CGA) programs refer to hospital-based settings. However the body of geriatric healthcare is provided by general practitioners in their office. Structured geriatric problem detection by means of assessment instruments is crucial for efficient geriatric care giving in the community. METHODS: We developed and pilot tested a German language geriatric assessment instrument adapted for general practice. Nine general practices in a rural region of Austria participated in this cross-sectional study and consecutively enrolled 115 persons aged over 75 years. The prevalence of specific geriatric problems was assessed, as well as the frequency of initiated procedures following positive and negative tests. Whether findings were new to the physician was studied exemplarily for the items visual and hearing impairment and depression. The acceptability was recorded by means of self-administered questionnaires. RESULTS: On average, each patient reported 6.4 of 14 possible geriatric problems and further consequences resulted in 43.7% (27.5% to 59.8%) of each problem. The items with either the highest prevalence and/or the highest number of initiated actions by the GPs were osteoporosis risk, urinary incontinence, decreased hearing acuity, missing pneumococcal vaccination and fall risk. Visual impairment was newly detected in only 18% whereas hearing impairment and depression was new to the physician in 74.1% and 76.5%, respectively.A substantial number of interventions were initiated not only following positive tests (43.7% per item; 95% CI 27.5% to 59.8%), but also as a consequence of negative test results (11.3% per item; 95% CI 1.7% to 20.9%). The mean time expenditure to accomplish the assessment was 31 minutes (SD 10 min). Patients (89%) and all physicians confirmed the CGA to provide new information in general on the patient's health status. All physicians judged the CGA to be feasible in everyday practice. CONCLUSION: This adapted CGA was feasible and well accepted in the general practice sample. High frequencies of geriatric problems were detected prompting high numbers of problem-solving initiatives. But a substantial number of actions of the physicians following negative tests point to the risks of too aggressive treatment of elderly patients with possibly subsequent negative effects.

Severe bronchopulmonary dysplasia improved by noninvasive positive pressure ventilation: a case report.

INTRODUCTION: This is the first report to describe the feasibility and effectiveness of noninvasive positive pressure ventilation in the secondary treatment of bronchopulmonary dysplasia. CASE PRESENTATION: A former male preterm of Caucasian ethnicity delivered at 29 weeks gestation developed severe bronchopulmonary dysplasia. At the age of six months he was in permanent tachypnea and dyspnea and in need of 100% oxygen with a flow of 2.0 L/minute via a nasal cannula. Intermittent nocturnal noninvasive positive pressure ventilation was then administered for seven hours daily. The ventilator was set at a positive end-expiratory pressure of 6 cmH2O, with pressure support of 4 cmH2O, trigger at 1.4 mL/second, and a maximum inspiratory time of 0.7 seconds. Over the course of seven weeks, the patient's maximum daytime fraction of inspired oxygen via nasal cannula decreased from 1.0 to 0.75, his respiratory rate from 64 breaths/minute to 50 breaths/minute and carbon dioxide from 58 mmHg to 44 mmHg. CONCLUSION: Noninvasive positive pressure ventilation may be a novel therapeutic option for established severe bronchopulmonary dysplasia. In the case presented, noninvasive positive pressure ventilation achieved sustained improvement in ventilation and thus prepared our patient for safe home oxygen therapy.

Nasal continuous positive airway pressure (n-CPAP) does not change cardiac output in preterm infants.

Our objective was to study how invasive mechanical ventilation impairs cardiac output (CO) in children and adults. Although the application of continuous positive airway pressure (CPAP) is widely practiced in neonatal intensive care, its hemodynamic consequences have not yet been investigated. A prospective study to assess the hemodynamic effects was conducted in 21 preterm infants < 1500 g using two-dimensional M-mode and pulsed Doppler echocardiography during and 1 hour after discontinuation of nasal CPAP (n-CPAP). Gestational age was 28.0 +/- 1.9 weeks (mean +/- standard deviation); birthweight, 1000 +/- 238 g; age at study entry, 200 +/- 155 hours; total maintenance fluid, 154 +/- 42 mL/kg/day; and n-CPAP level, 4.4 +/- 0.9 cm H(2)O. None of the infants received inotropic support, and n-CPAP did not cause any significant difference in the parameters measured: stroke volume, 3.1 +/- 1.0 mL (with n-CPAP) versus 3.1 +/- 1.0 mL (without n-CPAP); cardiac output, 487 +/- 156 mL/minute versus 500 +/- 176 mL/minute; left ventricular diastolic diameter, 1.22 +/- 0.15 cm versus 1.24 +/- 0.14 cm; fractional shortening, 0.30 +/- 0.05% versus 0.29 +/- 0.04%; and aortic velocity-time integral, 8.64 +/- 1.80 cm versus 8.70 +/- 1.65 cm. The n-CPAP level did not influence CO; n-CPAP (up to 7 cm H (2)O) has no echocardiographically detectable hemodynamic effect in preterm infants. Our data imply there is no need to withhold n-CPAP support to prevent circulatory compromise in these infants.

Genetic alterations in the tyrosine kinase transcriptome of human cancer cell lines.

Protein tyrosine kinases (PTKs) play a critical role in the manifestation of cancer cell properties, and respective signaling mechanisms have been studied extensively on immortalized tumor cells. To characterize and analyze commonly used cancer cell lines with regard to variations in the primary structure of all expressed PTKs, we conducted a cDNA-based sequence analysis of the entire tyrosine kinase transcriptome of 254 established tumor cell lines. The profiles of cell line intrinsic PTK transcript alterations and the evaluation of 155 identified polymorphisms and 234 somatic mutations are made available in a database designated "Tykiva" (tyrosine kinome variant). Tissue distribution analysis and/or the localization within defined protein domains indicate functional relevance of several genetic alterations. The cysteine replacement of the highly conserved Y367 residue in fibroblast growth factor receptor 4 or the Q26X nonsense mutation in the tumor-suppressor kinase CSK are examples, and may contribute to cell line-specific signaling characteristics and tumor progression. Moreover, known variants, such as epidermal growth factor receptor G719S, that were shown to mediate anticancer drug sensitivity could be detected in other than the previously reported tumor types. Our data therefore provide extensive system information for the design and interpretation of cell line-based cancer research, and may stimulate further investigations into broader clinical applications of current cancer therapeutics.

Measurements of the alpha factor of a distributed-feedback quantum cascade laser by an optical feedback self-mixing technique.

We demonstrate measurements of the alpha factor of a distributed-feedback quantum cascade laser (QCL) by using a newly modified self-mixing interferometric technique exploring the laser itself as the detector. We find a strong dependence of the alpha factor on the injection current, ranging from -0.44 at 120 mA to 2.29 at 180 mA, which can be attributed to the inherent physics of QCLs.