Fermentation Analytical Technology (FAT): Monitoring industrial E. coli fermentations using absolute quantitative 1H NMR spectroscopy.

BACKGROUND: To perform fast, reproducible, and absolute quantitative measurements in an automated manner has become of paramount importance when monitoring industrial processes, including fermentations. Due to its numerous advantages - including its inherent quantitative nature - Proton Nuclear Magnetic Resonance (1H NMR) spectroscopy provides an ideal tool for the time-resolved monitoring of fermentations. However, analytical conditions, including non-automated sample preparation and long relaxation times (T1) of some metabolites, can significantly lengthen the experimental time and make implementation in an industrial set up unfeasible. RESULTS: We present a high throughput method based on Standard Operating Procedures (SOPs) and 1H NMR, which lays the foundation for what we call Fermentation Analytical Technology (FAT). Our method was developed for the accurate absolute quantification of metabolites produced during Escherichia coli industrial fermentations. The method includes: (1) a stopped flow system for non-invasive sample collection followed by sample quenching, (2) automatic robot-assisted sample preparation, (3) fast 1H NMR measurements, (4) metabolites quantification using multivariate curve resolution (MCR), and (5) metabolites absolute quantitation using a novel correction factor (k) to compensate for the short recycle delay (D1) employed in the 1H NMR measurements. The quantification performance was tested using two sample types: buffer solutions of chemical standards and real fermentation samples. Five metabolites - glucose, acetate, alanine, phenylalanine and betaine - were quantified. Absolute quantitation ranged between 0.64 and 3.40 mM in pure buffer, and 0.71-7.76 mM in real samples. SIGNIFICANCE: The proposed method is generic and can be straight forward implemented to other types of fermentations, such as lactic acid, ethanol and acetic acid fermentations. It provides a high throughput automated solution for monitoring fermentation processes and for quality control through absolute quantification of key metabolites in fermentation broth. It can be easily implemented in an at-line industrial setting, facilitating the optimization of the manufacturing process towards higher yields and more efficient and sustainable use of resources.

Importance of familial predisposition to heart failure to the risk of anthracycline-related cardiotoxicity: A nationwide study.

BACKGROUND: Anthracycline-based chemotherapy has improved the prognosis of various malignancies, but increases the long-term risk of heart failure (HF). Identification of patients at risk prior to treatment initiation is warranted. Therefore, the aim of this study was to evaluate if a familial predisposition to HF increases the risk of anthracycline related HF. METHODS: Using nationwide Danish registries, all patients treated with anthracycline from 2004 to 16 were identified. The primary outcome was long-term HF risk. First-degree relatives were identified in the Danish Family Registry and exposure was defined as a first-degree biological relative with prior HF. Risk of HF was evaluated in a cumulative incidence function and the association in a multivariable Cox regression model. RESULTS: A total of 11,651 patients (median age 49.1 years (IQR: 43.6-53.7), 12.2% male) were included after exclusion of 46 with preanthracycline HF. Median follow-up was 3.8 years (IQR 1.9-6.4). In the group with a first-degree relative with HF (n = 1,608) 35 patients (2.2%) were diagnosed with HF vs 133 (1.3%) in the group without a first-degree relative with HF (n = 10,043), corresponding to incidence rates per 1,000 patient-years of 5.2 (CI:3.8-7.3) vs 3.0 (CI:2.5-3.5). The cumulative incidence of HF after 10 years was higher in the first-degree relative group (3.2% vs 2.0%, P = .004); adjusted hazard ratio 1.53 (CI:1.05-2.23, P = .03). CONCLUSION: In this nationwide register-based study having a first-degree relative with HF was associated with increased risk of anthracycline related HF, suggesting that attention towards family predisposition may be warranted when estimating the risk of anthracycline related cardiotoxicity.

Was the Late Ordovician mass extinction truly exceptional?

The Late Ordovician mass extinction event is the oldest of the five great extinction events in the fossil record. It has long been regarded as an outlier among mass extinctions, primarily due to its association with a cooling climate. However, recent temporally better resolved fossil biodiversity estimates complicate this view, providing growing evidence for a prolonged but punctuated biodiversity decline modulated by changes in atmospheric composition, ocean chemistry, and viable habitat area. This evolving view invokes extinction drivers similar to those that occurred during other major extinctions; some are even factors in the current human-induced biodiversity crisis. Even this very ancient and, at first glance, exceptional event conveys important lessons about the intensifying 'sixth mass extinction'.

Stable ocean redox during the main phase of the Great Ordovician Biodiversification Event.

The Great Ordovician Biodiversification Event (GOBE) represents the greatest increase in marine animal biodiversity ever recorded. What caused this transformation is heavily debated. One hypothesis states that rising atmospheric oxygen levels drove the biodiversification based on the premise that animals require oxygen for their metabolism. Here, we present uranium isotope data from a Middle Ordovician marine carbonate succession that shows the steepest rise in generic richness occurred with global marine redox stability. Ocean oxygenation ensued later and could not have driven the biodiversification. Stable marine anoxic zones prevailed during the maximum increase in biodiversity (Dapingian-early Darriwilian) when the life expectancy of evolving genera greatly increased. Subsequently, unstable ocean redox conditions occurred together with a marine carbon cycle disturbance and a decrease in relative diversification rates. Therefore, we propose that oceanic redox stability was a factor in facilitating the establishment of more resilient ecosystems allowing marine animal life to radiate.

Synchronizing rock clocks in the late Cambrian.

The Cambrian is the most poorly dated period of the past 541 million years. This hampers analysis of profound environmental and biological changes that took place during this period. Astronomically forced climate cycles recognized in sediments and anchored to radioisotopic ages provide a powerful geochronometer that has fundamentally refined Mesozoic-Cenozoic time scales but not yet the Palaeozoic. Here we report a continuous astronomical signal detected as geochemical variations (1 mm resolution) in the late Cambrian Alum Shale Formation that is used to establish a 16-Myr-long astronomical time scale, anchored by radioisotopic dates. The resulting time scale is biostratigraphically well-constrained, allowing correlation of the late Cambrian global stage boundaries with the 405-kyr astrochronological framework. This enables a first assessment, in numerical time, of the evolution of major biotic and abiotic changes, including the end-Marjuman extinctions and the Steptoean Positive Carbon Isotope Excursion, that characterized the late Cambrian Earth.

Middle Ordovician astrochronology decouples asteroid breakup from glacially-induced biotic radiations.

Meso-Cenozoic evidence suggests links between changes in the expression of orbital changes and millennia-scale climatic- and biotic variations, but proof for such shifts in orbital cyclicity farther back in geological time is lacking. Here, we report a 469-million-year-old Palaeozoic energy transfer from precession to 405 kyr eccentricity cycles that coincides with the start of the Great Ordovician Biodiversification Event (GOBE). Based on an early Middle Ordovician astronomically calibrated cyclostratigraphic framework we find this orbital change to succeed the onset of icehouse conditions by 200,000 years, suggesting a climatic origin. Recently, this icehouse was postulated to be facilitated by extra-terrestrial dust associated with an asteroid breakup. Our timescale, however, shows the meteor bombardment to post-date the icehouse by 800,000 years, instead pausing the GOBE 600,000 years after its initiation. Resolving Milankovitch cyclicity in deep time thus suggests universal orbital control in modulating climate, and maybe even biodiversity accumulation, through geological time.

suPAR Cut-Offs for Risk Stratification in Patients With Symptoms of COVID-19.

OBJECTIVES: Elevated soluble urokinase Plasminogen Activator Receptor (suPAR) is a biomarker associated with adverse outcomes. We aimed to investigate the associations between plasma suPAR levels (testing the cut-offs ⩽4, 4-6, and ⩾6 ng/mL) with risk of 14-day mortality, and with the risk of mechanical ventilation in patients that tested positive for SARS-CoV-2. METHODS: Observational cohort study of patients presenting with symptoms of COVID-19 at Department of Emergency Medicine, Amager and Hvidovre Hospital, Denmark from March 19th, 2020 to April 3rd, 2020. Plasma suPAR was measured using suPARnostic technologies. Patients were followed for development of mechanical ventilation and mortality for 14 days. Validation of our findings were carried out in a similar sized COVID-19 patient cohort from Mikkeli Central Hospital, Finland. RESULTS: Among 386 patients with symptoms of COVID-19, the median (interquartile range) age was 64 years (46-77), 57% were women, median suPAR was 4.0 ng/mL (2.7-5.9). In total, 35 patients (9.1%) died during the 14 days follow-up. Patients with suPAR ⩽4 ng/mL (N = 196; 50.8%) had a low risk of mortality (N = 2; 1.0%; negative predictive value of 99.0%, specificity 55.3%, sensitivity 95.2%, positive predictive value 17.4%). Among patients with suPAR ⩾6 ng/mL (N = 92; 23.8%), 16 died (17.4%). About 99 patients (25.6%) tested positive for SARS CoV-2 and of those 12 (12.1%) developed need for mechanical ventilation. None of the SARS-CoV-2 positive patients with suPAR ⩽4 ng/mL (N = 28; 38.8%) needed mechanical ventilation or died. The Mikkeli Central Hospital validation cohort confirmed our findings concerning suPAR cut-offs for risk of development of mechanical ventilation and mortality. CONCLUSIONS: Patients with symptoms of COVID-19 and suPAR ⩽4 or ⩾6 ng/mL had low or high risk, respectively, concerning the need for mechanical ventilation or mortality. We suggest cut-offs for identification of risk groups in patients presenting to the ED with symptoms of or confirmed COVID-19.

Population-based incidence and epidemiology of 5912 foot fractures.

BACKGROUND: The present study aimed to report a full overview of the incidence and epidemiology of foot fractures. METHOD: Population-based epidemiological cohort study including all foot fractures over 5 years. All patient charts and radiology were manually assessed. RESULTS: A total of 4938 patients sustained 5912 foot fractures during the study period. Patients' mean age at the time of fracture was 36.1 (21.7 SD) years. The overall incidence of foot fractures was 142.3/100,000/year. The hind foot incidence was 13.7/100,000/year, the mid foot incidence 6.5/100,000/year, and the fore foot incidence 123.9/100,000/year. The most common mode of injury was due to low energy trauma (98.7%). CONCLUSION: This study shows an overall incidence of foot fractures to be 142.3/100,000/year. The hind foot incidence is 13.7/100,000/year, the mid foot incidence 6.5/100,000/year, and the fore foot incidence 123.9/100,000/year.

Characteristics of patients with COVID-19 pneumonia at Hvidovre Hospital, March-April 2020.

INTRODUCTION: The first case of coronavirus disease 2019 (COVID-19) disease caused by severe acute respiratory syndrome coronavirus-2 occurred in Denmark on 27 February 2020. On 10 March, the first case of COVID-19 pneumonia was admitted to Hvidovre Hospital. METHODS: Retrospective case review of individuals 18 years or older who were admitted consecutively to Hvidovre Hospital from 10 March through 23 April 2020. RESULTS: A total of 175 individuals were admitted with COVID-19 pneumonia. The median age was 71 years, 48.6% were male and 71% had at least one co-morbidity. The most commonly presenting symptoms were dyspnoea, dry cough, and fever. The majority of patients had lymphopenia, elevated liver function tests and C-reactive protein. Nearly two in three presented with multilobar infiltration by chest X-ray. Respiratory failure leading to invasive mechanical ventilation developed in 27 patients (15.4%). By 20 April, 23 of 175 (13.1%) patients remained hospitalised, 43 (24.6%) had died and 109 (62.3%) had been discharged. CONCLUSIONS: The manifestations of COVID-19 at presentation were similar to those seen in other reports. Our population was older, slightly overrepresented by women and had a high level of co-morbidity. COVID-19 admittance was associated with frequent need of intensive care and mechanical ventilation that was associated with a very high mortality. FUNDING: none. TRIAL REGISTRATION: not relevant.

Building mountain biodiversity: Geological and evolutionary processes.

Mountain regions are unusually biodiverse, with rich aggregations of small-ranged species that form centers of endemism. Mountains play an array of roles for Earth's biodiversity and affect neighboring lowlands through biotic interchange, changes in regional climate, and nutrient runoff. The high biodiversity of certain mountains reflects the interplay of multiple evolutionary mechanisms: enhanced speciation rates with distinct opportunities for coexistence and persistence of lineages, shaped by long-term climatic changes interacting with topographically dynamic landscapes. High diversity in most tropical mountains is tightly linked to bedrock geology-notably, areas comprising mafic and ultramafic lithologies, rock types rich in magnesium and poor in phosphate that present special requirements for plant physiology. Mountain biodiversity bears the signature of deep-time evolutionary and ecological processes, a history well worth preserving.

The evolutionary dynamics of the early Palaeozoic marine biodiversity accumulation.

The early Palaeozoic Era records the initial biodiversification of the Phanerozoic. The increase in biodiversity involved drastic changes in taxon longevity, and in rates of origination and extinction. Here, we calculate these variables in unprecedented temporal resolution. We find that highly volatile origination and extinction rates are associated with short genus longevities during the Cambrian Period. During the Ordovician and Silurian periods, evolutionary rates were less volatile and genera persisted for increasingly longer intervals. The 90%-genus life expectancy doubled from 5 Myr in the late Cambrian to more than 10 Myr in the Ordovician-Silurian periods. Intervals with widespread ecosystem disruption are associated with short genus longevities during the Cambrian and with exceptionally high longevities during the Ordovician and Silurian periods. The post-Cambrian increase in persistence of genera, therefore, indicates an elevated ability of the changing early Palaeozoic marine ecosystems to sustainably maintain existing genera. This is evidence of a new level of ecosystem resilience which evolved during the Ordovician Period.

COPD exacerbations: the impact of long versus short courses of oral corticosteroids on mortality and pneumonia: nationwide data on 67 000 patients with COPD followed for 12 months.

Introduction: A large group of patients with chronic obstructive pulmonary disease (COPD) are exposed to an overload of oral corticosteroids (OCS) due to repeated exacerbations. This is associated with potential serious adverse effects. Therefore, we evaluated the impact of a recommended reduction of OCS duration in 2014 on the risk of pneumonia hospitalisation and all-cause mortality in patients with acute exacerbation of COPD (AECOPD). Methods: This was a nationwide observational cohort study that was based on linked administrative registry data between 1 January 2010 and 31 October 2017. 10 152 outpatients with COPD (median age 70 years) treated with either a short (≤250 mg) or long course (>250 mg) of OCS for AECOPD were included in the study. Cox proportional hazards regression models were used to derive an estimation of multivariable adjusted HRs (aHRs) for pneumonia hospitalisation or all-cause mortality combined and pneumonia hospitalisation and all-cause mortality, separately. Results: The long course of OCS treatment for AECOPD was associated with an increased 1-year risk of pneumonia hospitalisation or all-cause mortality (aHR 1.3, 95% CI 1.1 to 1.4; p<0.0001), pneumonia hospitalisation (aHR 1.2, 95% CI 1.0 to 1.3; p=0.0110) and all-cause mortality (aHR 1.8, 95% CI 1.5 to 2.2; p<0.0001) as compared with the short course of OCS treatment. These results were confirmed in several sensitivity analyses. Conclusion: The change of recommendations from long courses to short courses of OCS for AECOPD in 2014 was strongly associated with a decrease in pneumonia admissions and all-cause mortality, in favour of short courses of OCS.

Cascading trend of Early Paleozoic marine radiations paused by Late Ordovician extinctions.

The greatest relative changes in marine biodiversity accumulation occurred during the Early Paleozoic. The precision of temporal constraints on these changes is crude, hampering our understanding of their timing, duration, and links to causal mechanisms. We match fossil occurrence data to their lithostratigraphical ranges in the Paleobiology Database and correlate this inferred taxon range to a constructed set of biostratigraphically defined high-resolution time slices. In addition, we apply capture-recapture modeling approaches to calculate a biodiversity curve that also considers taphonomy and sampling biases with four times better resolution of previous estimates. Our method reveals a stepwise biodiversity increase with distinct Cambrian and Ordovician radiation events that are clearly separated by a 50-million-year-long period of slow biodiversity accumulation. The Ordovician Radiation is confined to a 15-million-year phase after which the Late Ordovician extinctions lowered generic richness and further delayed a biodiversity rebound by at least 35 million years. Based on a first-differences approach on potential abiotic drivers controlling richness, we find an overall correlation with oxygen levels, with temperature also exhibiting a coordinated trend once equatorial sea surface temperatures fell to present-day levels during the Middle Ordovician Darriwilian Age. Contrary to the traditional view of the Late Ordovician extinctions, our study suggests a protracted crisis interval linked to intense volcanism during the middle Late Ordovician Katian Age. As richness levels did not return to prior levels during the Silurian-a time of continental amalgamation-we further argue that plate tectonics exerted an overarching control on biodiversity accumulation.

PharmTeX: a LaTeX-Based Open-Source Platform for Automated Reporting Workflow.

Every year, the pharmaceutical industry generates a large number of scientific reports related to drug research, development, and regulatory submissions. Many of these reports are created using text processing tools such as Microsoft Word. Given the large number of figures, tables, references, and other elements, this is often a tedious task involving hours of copying and pasting and substantial efforts in quality control (QC). In the present article, we present the LaTeX-based open-source reporting platform, PharmTeX, a community-based effort to make reporting simple, reproducible, and user-friendly. The PharmTeX creators put a substantial effort into simplifying the sometimes complex elements of LaTeX into user-friendly functions that rely on advanced LaTeX and Perl code running in the background. Using this setup makes LaTeX much more accessible for users with no prior LaTeX experience. A software collection was compiled for users not wanting to manually install the required software components. The PharmTeX templates allow for inclusion of tables directly from mathematical software output as well and figures from several formats. Code listings can be included directly from source. No previous experience and only a few hours of training are required to start writing reports using PharmTeX. PharmTeX significantly reduces the time required for creating a scientific report fully compliant with regulatory and industry expectations. QC is made much simpler, since there is a direct link between analysis output and report input. PharmTeX makes available to report authors the strengths of LaTeX document processing without the need for extensive training. Graphical Abstract ᅟ.

Identifying the most surprising victims of mass extinction events: an example using Late Ordovician brachiopods.

Mass extinction events are recognized by increases in extinction rate and magnitude and, often, by changes in the selectivity of extinction. When considering the selective fingerprint of a particular event, not all taxon extinctions are equally informative: some would be expected even under a 'background' selectivity regime, whereas others would not and thus require special explanation. When evaluating possible drivers for the extinction event, the latter group is of particular interest. Here, we introduce a simple method for identifying these most surprising victims of extinction events by training models on background extinction intervals and using these models to make per-taxon assessments of 'expected' risk during the extinction interval. As an example, we examine brachiopod genus extinctions during the Late Ordovician Mass Extinction and show that extinction of genera in the deep-water 'Foliomena fauna' was particularly unexpected given preceding Late Ordovician extinction patterns.

Biogeographic and bathymetric determinants of brachiopod extinction and survival during the Late Ordovician mass extinction.

The Late Ordovician mass extinction (LOME) coincided with dramatic climate changes, but there are numerous ways in which these changes could have driven marine extinctions. We use a palaeobiogeographic database of rhynchonelliform brachiopods to examine the selectivity of Late Ordovician-Early Silurian genus extinctions and evaluate which extinction drivers are best supported by the data. The first (latest Katian) pulse of the LOME preferentially affected genera restricted to deeper waters or to relatively narrow (less than 35°) palaeolatitudinal ranges. This pattern is only observed in the latest Katian, suggesting that it reflects drivers unique to this interval. Extinction of exclusively deeper-water genera implies that changes in water mass properties such as dissolved oxygen content played an important role. Extinction of genera with narrow latitudinal ranges suggests that interactions between shifting climate zones and palaeobiogeography may also have been important. We test the latter hypothesis by estimating whether each genus would have been able to track habitats within its thermal tolerance range during the greenhouse-icehouse climate transition. Models including these estimates are favoured over alternative models. We argue that the LOME, long regarded as non-selective, is highly selective along biogeographic and bathymetric axes that are not closely correlated with taxonomic identity.

Onset of main Phanerozoic marine radiation sparked by emerging Mid Ordovician icehouse.

The Great Ordovician Biodiversification Event (GOBE) was the most rapid and sustained increase in marine Phanerozoic biodiversity. What generated this biotic response across Palaeozoic seascapes is a matter of debate; several intrinsic and extrinsic drivers have been suggested. One is Ordovician climate, which in recent years has undergone a paradigm shift from a text-book example of an extended greenhouse to an interval with transient cooling intervals - at least during the Late Ordovician. Here, we show the first unambiguous evidence for a sudden Mid Ordovician icehouse, comparable in magnitude to the Quaternary glaciations. We further demonstrate the initiation of this icehouse to coincide with the onset of the GOBE. This finding is based on both abiotic and biotic proxies obtained from the most comprehensive geochemical and palaeobiological dataset yet collected through this interval. We argue that the icehouse conditions increased latitudinal and bathymetrical temperature and oxygen gradients initiating an Early Palaeozoic Great Ocean Conveyor Belt. This fuelled the GOBE, as upwelling zones created new ecospace for the primary producers. A subsequent rise in δ(13)C ratios known as the Middle Darriwilian Isotopic Carbon Excursion (MDICE) may reflect a global response to increased bioproductivity encouraged by the onset of the GOBE.

Spatial distribution of soluble insulin in pig subcutaneous tissue: Effect of needle length, injection speed and injected volume.

The spatial distribution of a soluble insulin formulation was visualized and quantified in 3-dimensions using X-ray computed tomography. The drug distribution was visualized for ex vivo injections in pig subcutaneous tissue. Pig subcutaneous tissue has very distinct layers, which could be separated in the tomographic reconstructions and the amount of drug in each tissue class was quantified. With a scan time of about 45min per sample, and a robust segmentation it was possible to analyze differences in the spatial drug distribution between several similar injections. It was studied how the drug distribution was effected by needle length, injection speed and injected volume. For an injected volume of 0.1ml and injection depth of 8mm about 50% of the injections were partly intramuscular. Using a 5mm needle resulted in purely subcutaneous injections with minor differences in the spatial drug distribution between injections. Increasing the injected volume from 0.1ml to 1ml did not increase the intramuscular volume fraction, but gave a significantly higher volume fraction placed in the fascia separating the deep and superficial subcutaneous fat layers. Varying the injection speed from 25l/s up to 300l/s gave no changes in the drug concentration distribution. The method presented gives novel insight into subcutaneous injections of soluble insulin drugs and can be used to optimize the injection technique for subcutaneous drug administration in preclinical studies of rodents.

Insulin aspart pharmacokinetics: an assessment of its variability and underlying mechanisms.

BACKGROUND: Insulin aspart (IAsp) is used by many diabetics as a meal-time insulin to control post-prandial glucose levels. As is the case with many other insulin types, the pharmacokinetics (PK), and consequently the pharmacodynamics (PD), is associated with clinical variability, both between and within individuals. The present article identifies the main physiological mechanisms that govern the PK of IAsp following subcutaneous administration and quantifies them in terms of their contribution to the overall variability. MATERIAL AND METHODS: CT scanning data from Thomsen et al. (2012) are used to investigate and quantify the properties of the subcutaneous depot. Data from Brange et al. (1990) are used to determine the effects of insulin chemistry in subcutis on the absorption rate. Intravenous (i.v.) bolus and infusion PK data for human insulin are used to understand and quantify the systemic distribution and elimination (Pørksen et al., 1997; Sjöstrand et al., 2002). PK and PD profiles for type 1 diabetics from Chen et al. (2005) are analyzed to demonstrate the effects of IAsp antibodies in terms of bound and unbound insulin. PK profiles from Thorisdottir et al. (2009) and Ma et al. (2012b) are analyzed in the nonlinear mixed effects software Monolix® to determine the presence and effects of the mechanisms described in this article. RESULTS: The distribution of IAsp in the subcutaneous depot show an initial dilution of approximately a factor of two in a single experiment. Injected insulin hexamers exist in a chemical equilibrium with monomers and dimers, which depends strongly on the degree of dilution in subcutis, the presence of auxiliary substances, and a variety of other factors. Sensitivity to the initial dilution in subcutis can thus be a cause of some of the variability. Temporal variations in the PK are explained by variations in the subcutaneous blood flow. IAsp antibodies are found to be a large contributor to the variability of total insulin PK in a study by Chen et al. (2005), since only the free fraction is eliminated via the receptors. The contribution of these and other sources of variability to the total variability is quantified via a population PK analysis and two recent clinical studies (Thorisdottir et al., 2009; Ma et al., 2012b), which support the presence and significance of the identified mechanisms. CONCLUSIONS: IAsp antibody binding, oligomeric transitions in subcutis, and blood flow dependent variations in absorption rate seem to dominate the PK variability of IAsp. It may be possible via e.g. formulation design to reduce some of these variability factors.