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Global landscapes are changing due to human activities with consequences for both biodiversity and ecosystems. For single species, terrestrial mammal population densities have shown mixed responses to human pressure, with both increasing and decreasing densities reported in the literature. How the impacts of human activities on mammal populations translates into altered global density patterns remains unclear. Here we aim to disentangle the effect of human impacts on large-scale patterns of mammal population densities using a global dataset of 6729 population density estimates for 468 mammal species (representing 59% and 44% of mammalian orders and families). We fitted a mixed effect model to explain the variation in density based on a 1-degree resolution as a function of the human footprint index (HFI), a global proxy of direct and indirect human disturbances, while accounting for body mass, trophic level and primary productivity (normalized vegetation index; NDVI). We found a significant positive relationship between population density and HFI, where population densities were higher in areas with a higher HFI (e.g. agricultural or suburban areas – no populations were located in very high HFI urban areas) compared to areas with a low HFI (e.g. wilderness areas). We also tested the effect of the individual components of the HFI and still found a consistent positive effect. The relationships remained positive even across populations of the same species, although variability among species was high. Our results indicate shifts in mammal population densities in human modified landscapes, which is due to the combined effect of species filtering, increased resources and a possible reduction in competition and predation. Our study provides further evidence that macroecological patterns are being altered by human activities, where some species will benefit from these activities, while others will be negatively impacted or even extirpated.
Background: Breast cancer is the leading cause of cancer-related deaths in women, demanding new treatment options. With the advent of immune checkpoint blockade, immunotherapy emerged as a treatment option. In addition to lymphocytes, tumor-associated macrophages exert a significant, albeit controversial, impact on tumor development. Pro-inflammatory macrophages are thought to hinder, whereas anti-inflammatory macrophages promote tumor growth. However, molecular markers to identify prognostic macrophage populations remain elusive. Methods: We isolated two macrophage subsets, from 48 primary human breast tumors, distinguished by the expression of CD206. Their transcriptomes were analyzed via RNA-Seq, and potential prognostic macrophage markers were validated by PhenOptics in tissue microarrays of patients with invasive breast cancer. Results: Normal human breast tissue contained mainly CD206+ macrophages, while increased relative amounts of CD206− macrophages were observed in tumors. The presence of CD206+ macrophages correlated with a pronounced lymphocyte infiltrate and subsets of CD206+ macrophages, expressing SERPINH1 and collagen 1, or MORC4, were unexpectedly associated with improved survival of breast cancer patients. In contrast, MHCIIhi CD206− macrophages were linked with a poor survival prognosis. Conclusion: Our data highlight the heterogeneity of tumor-infiltrating macrophages and suggest the use of multiple phenotypic markers to predict the impact of macrophage subpopulations on cancer prognosis. We identified novel macrophage markers that correlate with the survival of patients with invasive mammary carcinoma.
Aims: Systemic inflammatory response, identified by increased total leucocyte counts, was shown to be a strong predictor of mortality after transcatheter aortic valve implantation (TAVI). Yet the mechanisms of inflammation-associated poor outcome after TAVI are unclear. Therefore, the present study aimed at investigating individual inflammatory signatures and functional heterogeneity of circulating myeloid and T-lymphocyte subsets and their impact on 1 year survival in a single-centre cohort of patients with severe aortic stenosis undergoing TAVI. Methods and results: One hundred twenty-nine consecutive patients with severe symptomatic aortic stenosis admitted for transfemoral TAVI were included. Blood samples were obtained at baseline, immediately after, and 24 h and 3 days after TAVI, and these were analysed for inflammatory and cardiac biomarkers. Myeloid and T-lymphocyte subsets were measured using flow cytometry. The inflammatory parameters were first analysed as continuous variables; and in case of association with outcome and area under receiver operating characteristic (ROC) curve (AUC) ≥ 0.6, the values were dichotomized using optimal cut-off points. Several baseline inflammatory parameters, including high-sensitivity C-reactive protein (hsCRP; HR = 1.37, 95% CI: 1.15–1.63; P < 0.0001) and IL-6 (HR = 1.02, 95% CI: 1.01–1.03; P = 0.003), lower counts of Th2 (HR = 0.95, 95% CI: 0.91–0.99; P = 0.009), and increased percentages of Th17 cells (HR = 1.19, 95% CI: 1.02–1.38; P = 0.024) were associated with 12 month all-cause mortality. Among postprocedural parameters, only increased post-TAVI counts of non-classical monocytes immediately after TAVI were predictive of outcome (HR = 1.03, 95% CI: 1.01–1.05; P = 0.003). The occurrence of SIRS criteria within 48 h post-TAVI showed no significant association with 12 month mortality (HR = 0.57, 95% CI: 0.13–2.43, P = 0.45). In multivariate analysis of discrete or dichotomized clinical and inflammatory variables, the presence of diabetes mellitus (HR = 3.50; 95% CI: 1.42–8.62; P = 0.006), low left ventricular (LV) ejection fraction (HR = 3.16; 95% CI: 1.35–7.39; P = 0.008), increased baseline hsCRP (HR = 5.22; 95% CI: 2.09–13.01; P < 0.0001), and low baseline Th2 cell counts (HR = 8.83; 95% CI: 3.02–25.80) were significant predictors of death. The prognostic value of the linear prediction score calculated of these parameters was superior to the Society of Thoracic Surgeons score (AUC: 0.88; 95% CI: 0.78–0.99 vs. 0.75; 95% CI: 0.64–0.86, respectively; P = 0.036). Finally, when analysing LV remodelling outcomes, ROC curve analysis revealed that low numbers of Tregs (P = 0.017; AUC: 0.69) and increased Th17/Treg ratio (P = 0.012; AUC: 0.70) were predictive of adverse remodelling after TAVI. Conclusions: Our findings demonstrate an association of specific pre-existing inflammatory phenotypes with increased mortality and adverse LV remodelling after TAVI. Distinct monocyte and T-cell signatures might provide additive biomarkers to improve pre-procedural risk stratification in patients referred to TAVI for severe aortic stenosis.
This study presents an ultra-wideband, elliptical slot, planar monopole antenna for early breast cancer microwave imaging. The on-body antenna's operation is optimised by direct contact with the patient's skin. With a compact size of 9 × 7 mm, the antenna covers a wide bandwidth from 16 to 24 GHz for reflection coefficients lower than –10 dB. Besides, it also features an electrode for electrical impedance tomography applications. Verification on a volunteer's breast gives an excellent agreement with the simulation for the defined bandwidth. Furthermore, as the first stage of the system's characterisation, pork fat is also used to demonstrate the possibility to enhance the transmission between the antennas within the high loss environment. Those results propose the feasibility of implementing a high-frequency radar system for breast cancer detection.
Today in the United States, the notion that ‘the rise of the far right’ poses the greatest threat to democratic values, and by extension, to the nation itself, has slowly entered into common sense. The antecedent of this development is the object of our study. Explored through the prism of what we refer to as the domestication of the War on Terror, this publication adopts and updates the theoretical approach first forwarded in Policing the Crisis: Mugging, the State, the Law and Order (Hall et al. 1978). Drawing on this seminal work, a sequence of three disparate media events are explored as they unfold in the United States in mid-2015: the rise of the Trump campaign; the release of an op-ed in The New York Times warning of a rise in right-wing extremsim; and a mass shooting at a historic African American church in Charleston, South Carolina. By the end of 2015, as these disparate events converge into what we call the public face of the rise of the far right phenomenon, we subsequently turn our attention to its origins in policing and the law in the wake of the global War on Terror and the Great Recession. It is only from there, that we turn our attention to the poltical class struggle as expressed in the rise of 'populism' on the one hand, and the domestication of the War on Terror on the other, and in doing so, attempt to situate the role of the rise of the far right phenomenon within it.
One of the most important events in human history occurred during the Early Pleistocene: the dispersal of early hominins out of Africa and into Europe and Asia. In Western Europe, the earliest evidences of the genus Homo have been found in the Baza Basin, at the sites of Orce in the SE of the Iberian Peninsula. These sites contain fossils and lithic industry dated approximately as 1.4–1.3 Ma.While hominin remains and artifacts at Orce, as well as the accompanying fauna, have been extensively studied, the properties and evolution of the Early Pleistocene vegetation in the basin remain unknown. The general effect of climate change on the expansion of early hominins from Africa into Eurasia still remains unclear. It is not known if the Early Pleistocene climate changes and the development of glacials periods led to the extirpation of European communities, or if those communities were able to endure and persist through such adverse climatic periods. This open question highlights the need for climate and environmental analyses for the time before, during and after the first presence of Homo in Europe. This PhD thesis contributes to that need by the presentation of the first long pollen record of the Baza Basin, where the oldest hominin sites in Western Europe are found.
This article provides a comparative overview of phonological and phonetic differences of Mukrī Kurdish varieties and their geographical distribution. Based on the examined data, four distinct varieties can be distinguished. In each variety area, different phonological patterns are analyzed according to age, gender, and social groups in order to establish cross-regional and cross-generational developments in relation to specific phonological distributions and shifts. The variety regions which are examined in the present article include West Mukrī (representing an archaic form of Mukrī), Central Mukrī (representing a linguistically peripheral dialect), East Mukrī (representing mixed archaic and peripheral dialect features), and South Mukrī (sharing features of both Mukrī and Ardałānī). The study concludes that variation in the Mukrīyān region depends on phonological developments, which in turn are due to geographical and sociological factors. Moreover, contact-induced change and internal language development are also established as triggering factors distinguishing regional variants.
Aims: Inadequate treatment is one of the factors interfering with a successful social and working life. Among students, it can impair their health and learning progress. In the field of medicine the problem of inadequate treatment seems widespread. This study examines wether inadequate treatment in internships differs between medicine and other academic disciplines.
Method: Using a questionnaire, the frequency, forms and severity of inadequate treatment among students were compared between the disciplines of medicine, civil engineering and teaching.
Results: 69,3% of medical students reported inadequate treatment during their internships, about twice as many as students of other disciplines. The ratios of verbal, non-verbal and organisational inadequate treatment were similar between the different academic disciplines. However, medical students executed tasks without receiving sufficient safety precautions or training significantly more often (sevenfold) than students of other disciplines. In total however, the experienced incidents of inadequate treatment were seen as similarly severe across the different academic fields.
Conclusion: Inadequate treatment of students during internships is a larger problem in medicine than in civil engineering or teaching, particularly concerning the performance of unsafe tasks. With regard to the health of students and patients, inadequate treatment in the medical education should be tackled. Previous studies suggest that this goal can be achieved only through longtime extensive measures on the level of students, lecturers, faculty and teaching hospitals.
Thermoanaerobacter kivui ist ein thermophiles acetogenes Bakterium, das chemolithoautotroph auf CO2 unter Verwendung von molekularem H2 als Elektronendonor wächst und Acetat als Produkt über den Wood-Ljungdahl-Weg (WLP) bildet. Im WLP werden 2 Mol CO2 reduziert, um ein Mol Acetyl-CoA zu bilden. Erste Studien wurden durchgeführt, um die Physiologie von T. kivui zu verstehen. T. kivui wächst autotroph auf H2 + CO2 und nach Adaptation auch auf CO oder Syngas. T. kivui wächst ebenfalls auch in Minimalmedium ohne weitere Zugabe von Vitaminen, was es zu einem Biokatalysator mit hohem Potenzial für die Produktion von Chemikalien mit hohem Mehrwert macht. Heterotroph wächst T. kivui auf Glucose, Fructose, Mannose, Pyruvat oder Formiat. Kürzlich wurde beschrieben, dass T. kivui in der Lage ist, auf dem Zuckeralkohol Mannitol in Gegenwart und Abwesenheit von HCO3- (oder externem CO2) zu wachsen. Allerdings war das Wachstum in Abwesenheit von externem CO2 deutlich verlangsamt. Daher wurde in dieser Studie getestet, ob eine Zugabe von externem Formiat das "fehlende" CO2 kompensieren kann. In Kombination mit Formiat wurde das Wachstum auf Mannitol in CO2 und HCO3- freien definierten Medien bis zu einer maximalen OD600 von 2,34 und mit einer Verdopplungszeit von 2,0 ± 0,0 stimuliert, was dem Wachstumsverhalten auf Mannitol in Anwesenheit von CO2/HCO3- entsprach. In Abwesenheit von Formiat (oder CO2) erreichte T. kivui nur eine endgültige optische Dichte von bis zu 0,7 mit einer verlängerten Verdoppelungszeit von 5,2 ± 0,2 Stunden. Dieses Experiment zeigte die höhe metabolische Flexibilität von T. kivui durch die Nutzung von Formiat als Elektronenakzeptor, wenn kein oder nur wenig CO2 vorhanden ist.
Genomanalysen ergaben, dass T. kivui ein Trehalose- und Maltose-Transportsystem-Permeaseprotein (MalF) besitzt. Darüber hinaus verfügt T. kivui über Trehalose- und Maltosehydrolase-Gene, die als Kojibiose-Phosphorylase annotiert sind. Obwohl in der Originalveröffentlichung beschrieben wurde, dass der Organismus nicht auf Maltose oder Trehalose wachsen kann, konnte T. kivui im Laufe dieser Arbeit an das Wachstum auf Maltose und Trehalose adaptiert werden. Nach dem Transfer von einer Glukose-Vorkultur auf ein Medium mit 25 mM Maltose oder 25 mM Trehalose als alleinige C-Quelle wurde kein Wachstum erzielt. Bei Verwendung der gleichen Vorkultur in einem Medium mit höherer Konzentration (50 mM) Maltose oder Trehalose, begannen die Zellen zu wachsen. Bei Verwendung dieser adaptierten kulturen als Vorkultur wuchsen die Zellen in Gegenwart von in 25 mM Maltose oder Trehalose bis zu einer maximalen OD600 von 1,12 bzw. 0,73. Die Adaptation hing mit der Tatsache zusammen, dass der Organismus eine höhere Konzentration benötigt, um sich an diese Kohlenstoffquellen zu gewöhnen. Durch diese Daten wird das heterotrophe Potenzial von T. kivui erhöht.
Um die Bedeutung der wasserstoffabhängigen Kohlendioxidreduktase (HDCR) während des Wachstums auf Formiat oder auf H2 + CO2 im Stoffwechsel von T. kivui zu verstehen, wurden Studien auf molekularer Ebene durchgeführt. Die HDCR nutzt H2 direkt für die Reduktion von CO2 zu Formiat im ersten Schritt des Wood-Ljungdahl-Wegs (WLP). Um die Rolle der HDCR in dieser Reaktion zu untersuchen, wurde das hdcr-Gencluster mit Hilfe des kürzlich entwickelten Mutagenesytems für T. kivui deletiert. In Wachstumstudien konnte anschliessend gezeigt werden, dass die ߡhdcr-Deletionsmutante nicht mehr auf Formiat oder H2 + CO2 als alleiniger Kohlenstoffquelle wachsen konnte. Nach Komplementation der Mutante mit dem hdcr-Gene in cis wuchsen die Kulture wieder auf Formiat oder H2 + CO2. Diese Experimente zeigten, dass die HDCR für das Wachstum auf H2 + CO2 oder Formiat essentiell ist. Interessanterweise konnte in der ߡhdcr-Mutante ebenfalls ein verändertes Wachstum auf Glukose als alleiniger C-Quelle festgestellt werden. Die T. kivui ߡhdcr-Mutante wuchs nur bis zu einer OD600 von 0,2, während der Wildtyp und der hdcr-komplementierte Stamm bis zu einer OD600 von 2,64 bzw. 2,4 wuchsen. Damit wurde bewiesen, dass die HDCR auch für die vollständige Glukoseoxidation in T. kivui erforderlich ist. Durch die Zugabe von Formiat wurde das Wachstum vollständig wiederhergestellt, ähnlich wie beim Wildtyp. Dies belegt wieder die Nutzung Formiat als terminalen Elektronenakzeptor. Auch auf Mannitol oder Pyruvat konnte die Mutanten nur in Gegenwart von Formiat wachsen. Der Substratverbrauch und die Produktbildung der T. kivui ߡhdcr-Mutante wurden in einem Zellsuspensionsexperiment untersucht. Die Zellen verbrauchten Formiat nur in Gegenwart von Glukose und produzierten Acetat mit einem Acetat/Substrat-Verhältnis von etwas mehr als 3,0, während die Acetatproduktion nur 12 mM betrug, wenn Glukose als alleiniges Substrat verwendet wurde. Diese Ergebnisse zeigen eine enge Kopplung der Oxidation von Multikohlenstoffsubstraten an den WLP.
T. kivui ist eines der wenigen Acetogenen, die CO als einzige Kohlenstoff- und Energiequelle nutzen können. ...
For a class of Cannings models we prove Haldane’s formula, π(sN)∼2sNρ2, for the fixation probability of a single beneficial mutant in the limit of large population size N and in the regime of moderately strong selection, i.e. for sN∼N−b and 0<b<1/2. Here, sN is the selective advantage of an individual carrying the beneficial type, and ρ2 is the (asymptotic) offspring variance. Our assumptions on the reproduction mechanism allow for a coupling of the beneficial allele’s frequency process with slightly supercritical Galton–Watson processes in the early phase of fixation.
Current research on theory and practice of digital libraries: best papers from TPDL 2019 & 2020
(2022)
This volume presents a special issue on selected papers from the 2019 & 2020 editions of the International Conference on Theory and Practice of Digital Libraries (TPDL). They cover different research areas within Digital Libraries, from Ontology and Linked Data to quality in Web Archives and Topic Detection. We first provide a brief overview of both TPDL editions, and we introduce the selected papers.
The authors reflect on their experiences as the founding editors of the History of Knowledge blog. Situating the project in its specific institutional, geographical, and historiographical contexts, they highlight its role in scholarly communication and research alongside journals and books in a research domain that is still young, especially when viewed from an international perspective. At the same time, the authors discuss the blog’s role as a tool for classifying and structuring a corpus of work as it grows over time and as new themes and connections emerge from the contributions of its many authors.
More than 2 million tons of glycerol are produced during industrial processes each year and, therefore, glycerol is an inexpensive feedstock to produce biocommodities by bacterial fermentation. Acetogenic bacteria are interesting production platforms and there have been few reports in the literature on glycerol utilization by this ecophysiologically important group of strictly anaerobic bacteria. Here, we show that the model acetogen Acetobacterium woodii DSM1030 is able to grow on glycerol, but contrary to expectations, only for 2–3 transfers. Transcriptome analysis revealed the expression of the pdu operon encoding a propanediol dehydratase along with genes encoding bacterial microcompartments. Deletion of pduAB led to a stable growth of A. woodii on glycerol, consistent with the hypothesis that the propanediol dehydratase also acts on glycerol leading to a toxic end-product. Glycerol is oxidized to acetate and the reducing equivalents are reoxidized by reducing CO2 in the Wood–Ljungdahl pathway, leading to an additional acetate. The possible oxidation product of glycerol, dihydroxyacetone (DHA), also served as carbon and energy source for A. woodii and growth was stably maintained on that compound. DHA oxidation was also coupled to CO2 reduction. Based on transcriptome data and enzymatic analysis we present the first metabolic and bioenergetic schemes for glycerol and DHA utilization in A. woodii.
Autophagy is a highly conserved catabolic process cells use to maintain their homeostasis by degrading misfolded, damaged and excessive proteins, nonfunctional organelles, foreign pathogens and other cellular components. Hence, autophagy can be nonselective, where bulky portions of the cytoplasm are degraded upon stress, or a highly selective process, where preselected cellular components are degraded. To distinguish between different cellular components, autophagy employs selective autophagy receptors, which will link the cargo to the autophagy machinery, thereby sequestering it in the autophagosome for its subsequent degradation in the lysosome. Autophagy receptors undergo post-translational and structural modifications to fulfil their role in autophagy, or upon executing their role, for their own degradation. We highlight the four most prominent protein modifications – phosphorylation, ubiquitination, acetylation and oligomerisation – that are essential for autophagy receptor recruitment, function and turnover. Understanding the regulation of selective autophagy receptors will provide deeper insights into the pathway and open up potential therapeutic avenues.
The intriguing (μ-hydrido)diboranes(4) with their prominent pristine representative [B2H5]− have mainly been studied theoretically. We now describe the behavior of the planarized tetraaryl (μ-hydrido)diborane(4) anion [1H]− in cycloaddition reactions with the homologous series of heterocumulenes CO2, iPrNCO, and iPrNCNiPr. We show that a C=O bond of CO2 selectively activates the B−B bond of [1H]−, while the μ-H ligand is left untouched ([2H]−). The carbodiimide iPrNCNiPr, in contrast, neglects the B−B bond and rather adds the B-bonded H− ion to its central C atom to generate a formamidinate bridge across the B2 pair ([3]−). As a hybrid, the isocyanate iPrNCO combines the reactivity patterns of both its congeners and gives two products: one of them ([4H]−) is related to [2H]−, the other ([5]−) is an analog of [3]−. We finally propose a mechanistic scenario that rationalizes the individual reaction outcomes and combines them to a coherent picture of B–B vs. B–H bond activation.
Objectives: To compare radiation dose and image quality of single-energy (SECT) and dual-energy (DECT) head and neck CT examinations performed with second- and third-generation dual-source CT (DSCT) in matched patient cohorts. Methods: 200 patients (mean age 55.1 ± 16.9 years) who underwent venous phase head and neck CT with a vendor-preset protocol were retrospectively divided into four equal groups (n = 50) matched by gender and BMI: second (Group A, SECT, 100-kV; Group B, DECT, 80/Sn140-kV), and third-generation DSCT (Group C, SECT, 100-kV; Group D, DECT, 90/Sn150-kV). Assess- ment of radiation dose was performed for an average scan length of 27 cm. Contrast-to-noise ratio measure- ments and dose-independent figure-of-merit calcu- lations of the submandibular gland, thyroid, internal jugular vein, and common carotid artery were analyzed quantitatively. Qualitative image parameters were evalu- ated regarding overall image quality, artifacts and reader confidence using 5-point Likert scales. Results: Effective radiation dose (ED) was not signifi- cantly different between SECT and DECT acquisition for each scanner generation (p = 0.10). Significantly lower effective radiation dose (p < 0.01) values were observed for third-generation DSCT groups C (1.1 ± 0.2 mSv) and D (1.0 ± 0.3 mSv) compared to second-generation DSCT groups A (1.8 ± 0.1 mSv) and B (1.6 ± 0.2 mSv). Figure-of- merit/contrast-to-noise ratio analysis revealed superior results for third-generation DECT Group D compared to all other groups. Qualitative image parameters showed non-significant differences between all groups (p > 0.06). Conclusion: Contrast-enhanced head and neck DECT can be performed with second- and third-generation DSCT systems without radiation penalty or impaired image quality compared with SECT, while third-generation DSCT is the most dose efficient acquisition method. Advances in knowledge: Differences in radiation dose between SECT and DECT of the dose-vulnerable head and neck region using DSCT systems have not been evaluated so far. Therefore, this study directly compares radiation dose and image quality of standard SECT and DECT protocols of second- and third-generation DSCT platforms.
Endothelial tip cells are essential for VEGF-induced angiogenesis, but underlying mechanisms are elusive. The Ena/VASP protein family, consisting of EVL, VASP, and Mena, plays a pivotal role in axon guidance. Given that axonal growth cones and endothelial tip cells share many common features, from the morphological to the molecular level, we investigated the role of Ena/VASP proteins in angiogenesis. EVL and VASP, but not Mena, are expressed in endothelial cells of the postnatal mouse retina. Global deletion of EVL (but not VASP) compromises the radial sprouting of the vascular plexus in mice. Similarly, endothelial-specific EVL deletion compromises the radial sprouting of the vascular plexus and reduces the endothelial tip cell density and filopodia formation. Gene sets involved in blood vessel development and angiogenesis are down-regulated in EVL-deficient P5-retinal endothelial cells. Consistently, EVL deletion impairs VEGF-induced endothelial cell proliferation and sprouting, and reduces the internalization and phosphorylation of VEGF receptor 2 and its downstream signaling via the MAPK/ERK pathway. Together, we show that endothelial EVL regulates sprouting angiogenesis via VEGF receptor-2 internalization and signaling.
The cosmological implications of the Covariant Canonical Gauge Theory of Gravity (CCGG) are investigated. CCGG is a Palatini theory derived from first principles using the canonical transformation formalism in the covariant Hamiltonian formulation. The Einstein-Hilbert theory is thereby extended by a quadratic Riemann-Cartan term in the Lagrangian. Moreover, the requirement of covariant conservation of the stress-energy tensor leads to necessary presence of torsion. In the Friedman universe that promotes the cosmological constant to a time-dependent function, and gives rise to a geometrical correction with the EOS of dark radiation. The resulting cosmology, compatible with the ΛCDM parameter set, encompasses bounce and bang scenarios with graceful exits into the late dark energy era. Testing those scenarios against low-z observations shows that CCGG is a viable theory.
Consequences of minimal length discretization on line element, metric tensor, and geodesic equation
(2021)
When minimal length uncertainty emerging from a generalized uncertainty principle (GUP) is thoughtfully implemented, it is of great interest to consider its impacts on gravitational Einstein field equations (gEFEs) and to try to assess consequential modifications in metric manifesting properties of quantum geometry due to quantum gravity. GUP takes into account the gravitational impacts on the noncommutation relations of length (distance) and momentum operators or time and energy operators and so on. On the other hand, gEFE relates classical geometry or general relativity gravity to the energy–momentum tensors, that is, proposing quantum equations of state. Despite the technical difficulties, we intend to insert GUP into the metric tensor so that the line element and the geodesic equation in flat and curved space are accordingly modified. The latter apparently encompasses acceleration, jerk, and snap (jounce) of a particle in the quasi-quantized gravitational field. Finite higher orders of acceleration apparently manifest phenomena such as accelerating expansion and transitions between different radii of curvature and so on.
Objectives: The four-dimensional ultrasound (4D-US) enables imaging of the aortic segment and simultaneous determination of the wall expansion. The method shows a high spatial and temporal resolution, but its in vivo reliability is so far unknown for low-measure values. The present study determines the intraobserver repeatability and interobserver reproducibility of 4D-US in the atherosclerotic and non-atherosclerotic infrarenal aorta. Methods: In all, 22 patients with non-aneurysmal aorta were examined by an experienced examiner and a medical student. After registration of 4D images, both the examiners marked the aortic wall manually before the commercially implemented speckle tracking algorithm was applied. The cyclic changes of the aortic diameter and circumferential strain were determined with the help of custom-made software. The reliability of 4D-US was tested by the intraclass correlation coefficient (ICC). Results: The 4D-US measurements showed very good reliability for the maximum aortic diameter and the circumferential strain for all patients and for the non-atherosclerotic aortae (ICC >0.7), but low reliability for circumferential strain in calcified aortae (ICC = 0.29). The observer- and masking-related variances for both maximum diameter and circumferential strain were close to zero. Conclusions: Despite the low-measured values, the high spatial and temporal resolution of the 4D-US enables a reliable evaluation of cyclic diameter changes and circumferential strain in non-aneurysmal aortae independent from the observer experience but with some limitations for calcified aortae. The 4D-US opens up a new perspective with regard to noninvasive, in vivo assessment of kinematic properties of the vessel wall in the abdominal aorta.
Abstract: The Children's Communication Checklist-2 (CCC-2) is often applied to assess pragmatic language impairment which is highly prevalent in autism spectrum disorder (ASD) and several mental health conditions. We replicated previous findings on the limited applicability of the CCC-2 in clinical samples and the inconsistent findings concerning the factor structure. The aim of the present study was, thus, to develop a concise, simplified, and revised version of the CCC-2 in a large German-speaking sample. Four groups of children and adolescents aged 4 to 17 years were included: ASD (n = 195), intellectual disability (ID, n = 83), diverse mental health conditions (MHC, n = 144) and a typically developing control group (TD, n = 417). We reduced the original number of items from 70 to 39, based on item analysis, exploratory factor analysis and the exclusion of communication-unrelated items. The revised version, CCC-R (α = 0.96), consists of two empirically derived factors: a pragmatic-language (α = 0.96) and a grammatical-semantic-language factor (α = 0.93). All clinical groups (ASD, ID, and MHC) had significantly increased CCC-R total scores, with the highest scores being in the neurodevelopmental disorder groups (ASD and ID). In addition, we found group-specific patterns of elevated pragmatic-language scores in the ASD group and grammatical-semantic scores in the ID group. The CCC-R was comparable to the CCC-2 in distinguishing ASD from the other groups. The CCC-R is proposed as a simplified and easily applied, clinical questionnaire for caregivers, assessing pragmatic language impairments across neurodevelopmental disorders and mental health conditions. Lay Summary: The CCC-2 is a questionnaire designed to identify children who have problems in the social use of language, however, it is limited in its clinical application and exhibits inconsistent factors. We have created a shorter and simpler version of the CCC-2 that we have called the CCC-R which overcomes the previous limitations of the CCC-2. It consists of two subscales: pragmatic language and grammatical-semantic language. The CCC-R can be used as a short and clinically relevant caregiver questionnaire which assesses pragmatic language impairments in children and adolescents. Autism Res 2021, 14: 759–772. © 2021 The Authors. Autism Research published by International Society for Autism Research published by Wiley Periodicals LLC.
The crystal structures of sodium ethoxide (sodium ethanolate, NaOEt), sodium n-propoxide (sodium n-propanolate, NaOnPr), sodium n-butoxide (sodium n-butanolate, NaOnBu) and sodium n-pentoxide (sodium n-amylate, NaOnAm) were determined from powder X-ray diffraction data. NaOEt crystallizes in space group P421m, with Z = 2, and the other alkoxides crystallize in P4/nmm, with Z = 2. To resolve space-group ambiguities, a Bärnighausen tree was set up, and Rietveld refinements were performed with different models. In all structures, the Na and O atoms form a quadratic net, with the alkyl groups pointing outwards on both sides (anti-PbO type). The alkyl groups are disordered. The disorder becomes even more pronounced with increasing chain length. Recrystallization from the corresponding alcohols yielded four sodium alkoxide solvates: sodium ethoxide ethanol disolvate (NaOEt·2EtOH), sodium n-propoxide n-propanol disolvate (NaOnPr·2nPrOH), sodium isopropoxide isopropanol pentasolvate (NaOiPr·5iPrOH) and sodium tert-amylate tert-amyl alcohol monosolvate (NaOtAm·tAmOH, tAm = 2-methyl-2-butyl). Their crystal structures were determined by single-crystal X-ray diffraction. All these solvates form chain structures consisting of Na+, –O− and –OH groups, encased by alkyl groups. The hydrogen-bond networks diverge widely among the solvate structures. The hydrogen-bond topology of the iPrOH network in NaOiPr·5iPrOH shows branched hydrogen bonds and differs considerably from the networks in pure crystalline iPrOH.
Genetic engineering of Saccharomyces cerevisiae for improved cytosolic isobutanol biosynthesis
(2021)
The finite nature of fossil resources and the environmental problems caused by their excessive usage requires alternative approaches. The transformation from a fossil based economy to one based on renewable biomass is called a “bioeconomy”. To substitute fossil resources, various microorganisms have already been modified for the biosynthesis of valuable chemicals from biomass. However, the development of such efficient microorganisms at an industrial scale, remains a major challenge. The most prominent and robust microorganism for industrial production is the yeast Saccharomyces cerevisiae, which is known to produce ethanol that is used as renewable biofuel. However, S. cerevisiae is also naturally able to produce isobutanol in small amounts. Isobutanol is favoured as a biofuel compared to ethanol due to its higher octane number and lower hygroscopicity, which makes it more suitable for application in conventional combustion engines. In S. cerevisiae, the biosynthesis of isobutanol is permitted by the combination of mitochondrial valine synthesis (catalysed by Ilv2, Ilv5 and Ilv3) and its cytosolic degradation (catalysed by Aro10 and Adh2). The different compartmentalisation of the two pathways limit isobutanol biosynthesis. Thus, Brat et al. (2012) were able to increase the isobutanol yield up to 15 mg/gGlc by cytosolic re localisation of the enzymes Ilv2Δ54, Ilv5Δ48 and Ilv3Δ19 (cyt-ILV), with simultaneous deletion of ilv2. This corresponds to approximately 3.7% of the theoretical yield of 410 mg/gGlc, implying existing limitations in isobutanol biosynthesis, which have been investigated in this work.
For yet unknown reasons, isobutanol was only produced by S. cerevisiae in a valine free medium, according to Brat et al. (2012). This work shows that this can be attributed to the catalytic activity of Ilv2Δ54, which acted as growth inhibitor to S. cerevisiae. By this logic, a negative selection on the ILV2∆54 gene was exerted, which made the ilv2 deletion and simultaneous valine exclusion necessary to maintain the functional expression of toxic ILV2∆54. Furthermore, it was shown that valine exclusion is not mandatory due to the feedback regulation of Ilv2, permitted by Ilv6. Rather, increased isobutanol yield was observed when cytosolic Ilv6∆61 was expressed in the valine free medium, which is explained by the enhanced regulation of Ilv2Δ54 by Ilv6∆61 when BCAA are absent. Isobutanol biosynthesis is neither redox nor NAD(P)H co factor balanced. It was seen that co factor imbalance could be mitigated by the expression of an NADH oxidase (NOX), but not by expression of the NADH dependent ilvC6E6, since the latter showed low in vivo activity. Furthermore, it was seen that NAD(H) imbalance did already limit isobutanol biosynthesis, but the NADP(H) imbalance did not. Another limitation of cytosolic isobutanol biosynthesis is the secretion of the intermediate 2‑dihydroxyisovalerate, which then no longer is taken up by S. cerevisiae, causing a reduced isobutanol yield. This is attributed to insufficient Ilv3∆19 activity, due to poor iron sulphur cluster apo protein maturation. Therefore, it was aimed to replace Ilv3∆19 by heterologous dihydroxyacid dehydratases. Even though some of the enzymes were functionally expressed, none showed better in vivo activity than Ilv3∆19. Therefore, the Ilv3∆19 apo protein maturation was improved. This was achieved by the genomic deletion of fra2 or pim1 as well as by the cytosolic expression of Grx5∆29.
In addition to the isobutanol pathway, S. cerevisiae was optimised for isobutanol biosynthesis by rational and evolutionary engineering. For this purpose, the genes which are necessary for isobutanol production were integrated into the ilv2 locus, and the resulting strain was evolved in a medium containing the toxic amino acid analogue norvaline. Evolved single colonies were isolated, which presented improved growth and increased isobutanol yields (0.59 mg/gGlc) in a valine free medium, as compared to the initial strain. This is explained by a gene dosage effect which occurred during the evolutionary engineering experiment. In collaboration with Dr. Wess, the genes ilv2, bdh1/2, leu4/9, ecm31, ilv1, adh1, gpd1/2 and ald6 were cumulatively deleted in CEN.PK113 7D to block competing metabolic pathways. The resulting strain JWY23 achieved isobutanol yields up to 67.3 mg/gGlc, when expressing the cyt ILV enzymes from a multi copy vector. The most promising approaches of this work, namely the deletion of fra2 and the expression of Grx5∆29, Ilv6∆61, and NOX, were confirmed in this JWY23 strain. The highest isobutanol yield from this work was observed at 72 mg/gGlc for Ilv6∆61 and cyt ILV enzymes expressing JWY23, which corresponds to 17.6% of the theoretical isobutanol yield.
Isobutyric acid (IBA) is a by product of isobutanol biosynthesis, but it is also considered a valuable platform chemical. Therefore, the approaches that improved isobutanol biosynthesis were applied to the biosynthesis of IBA in S. cerevisiae. The highest IBA yield of 9.8 mg/gGlc was observed in a valine free medium by expression of cyt ILV enzymes, NOX and Ald6 in JWY04 (CEN.PK113 7D Δilv2; Δbdh1; Δbdh2; Δleu4; Δleu9; Δecm31; Δilv1). This corresponded to an 8.9 fold increase compared with the control and is, to our best knowledge, the highest IBA yield reported to date for S. cerevisiae.
Cytochrome c oxidases are among the most important and fundamental enzymes of life. Integrated into membranes they use four electrons from cytochrome c molecules to reduce molecular oxygen (dioxygen) to water. Their catalytic cycle has been considered to start with the oxidized form. Subsequent electron transfers lead to the E-state, the R-state (which binds oxygen), the P-state (with an already split dioxygen bond), the F-state and the O-state again. Here, we determined structures of up to 1.9 Å resolution of these intermediates by single particle cryo-EM. Our results suggest that in the O-state the active site contains a peroxide dianion and in the P-state possibly an intact dioxygen molecule, the F-state may contain a superoxide anion.
High-pressure single-crystal to 20 GPa and powder diffraction measurements to 50 GPa, show that the structure of Pb2SnO4 strongly distorts on compression with an elongation of one axis. A structural phase transition occurs between 10 GPa and 12 GPa, with a change of space group from Pbam to Pnam. The resistivity decreases by more than six orders of magnitude when pressure is increased from ambient conditions to 50 GPa. This insulator-to-semiconductor transition is accompanied by a reversible appearance change from transparent to opaque. Density functional theory-based calculations show that at ambient conditions the channels in the structure host the stereochemically-active Pb 6s2 lone electron pairs. On compression the lone electron pairs form bonds between Pb2+ ions. Also provided is an assignment of irreducible representations to the experimentally observed Raman bands.
Die Studien im Rahmen dieser Arbeit wurden am Modellorganismus Anabaena sp. PCC 7120 (Anabaena) durchgeführt, einem filamentösen Süßwasser-Cyanobakterium. Cyanobakterien sind photosynthetische, Gram-negative Organismen. Sie besitzen eine das Zytosol begrenzende Plasmamembran und eine Äußere Membran. TonB-abhängige Transporter (TBDTs) und Porine der Äußeren Membran bewerkstelligen und regulieren die Aufnahme von Nährstoffen. Typischerweise wenig abundante Substrate für den TBDT-vermittelten, aktiven Transport sind beispielsweise eisenhaltige Siderophore oder VitaminB12. Kleinere gelöste und abundante Stoffe wie Salze oder andere Ionen gelangen hingegen passiv durch Porine in das Periplasma.
In Anabaena wurden neun putative Porine identifiziert. Sieben hiervon wiesen eine porinspezifische Domänenstruktur auf (Alr0834, Alr2231, All4499, Alr4550, Alr4741, All5191 und All7614), und wurden im Rahmen dieser Arbeit näher betrachtet. Die Expression dieser sieben Gene wurde vergleichend untersucht, nachdem der Wildtyp in Standardmedium oder in Medium indem jeweils Mangan, Eisen, Kupfer oder Zink fehlte angezogen wurde. Außerdem wurde das Wachstum der einzelnen Porinmutanten im Vergleich zum Wildtyp auf Festmedium mit hohen Konzentrationen von Salzen, Antibiotika oder anderen Stoffen analysiert. Hierbei konnten den einzelnen Mutanten teilweise spezifische phänotypische Eigenschaften zugeschrieben werden. Zusammengefasst kann anhand der Analysenergebnisse vermutet werden, dass Alr4550 eine besondere Rolle in der Wahrung der Zellhüllenstabilität oder -integrität spielt, wohingegen das Fehlen von Alr5191 auf unbekannte Weise die Fixierung von Stickstoff zu erschweren scheint. Die alr2231-Mutante zeigte eine Resistenz gegenüber hohen Zinkkonzentrationen, was die Vermutung zulässt, dass Zink ein Substrat von Alr2231 darstellt. Für weitere Porine kann ebenfalls ein Zusammenhang zum Transport von Kupfer oder Mangan vermutet werden.
Neben Porinen wurden ebenfalls TonB-ähnliche Proteine in Anabaena untersucht. TonB ist ein plasmamembranständiges Protein, das in Komplex mit ExbB und ExbD die Energie für Transportprozesse über die Äußere Membran bereitstellt. Hierfür bindet TonB C-terminal an TBDTs und induziert dort Strukturänderungen, welche den Substratimport ins Periplasma ermöglichen. Als Energiequelle wird der Protonengradient genutzt, der über die Plasmamembran besteht. In Anabaena wurden vier putative TonB Proteine identifiziert, die sich jeweils in Länge und Domänenstruktur unterscheiden. Im Rahmen dieser Arbeit konnte durch Substrattransport-Experimente und Wachstumsanalysen gezeigt werden, dass TonB3 an der Aufnahme zweier Siderophore (Schizokinen und dem Xenosiderophor Ferrichrom) beteiligt ist, da die entsprechende Mutante sich als unfähig erwies diese zu als Eisenquelle nutzbar zu machen. Daneben wies TonB3 weitere Merkmale auf, die auch TonB-Proteinen anderer Organismen zugeschrieben wurden (Wachstumsdefizit der Mutante unter Eisenmangel, eisenabhängiges Expressionsprofil). Interessanterweise zeigte sich, dass das Siderophor Ferrichrom ebenfalls nicht als Eisenquelle für die tonB4-Mutante zur Verfügung stand, was zum Beispiel auf eine Beteiligung von TonB4 an dessen Transport hinweisen könnte.
TonB1, welches sich durch ein inkomplettes TBDT-Interaktionsmotiv auszeichnet, und TonB2 konnte keine Beteiligung am Siderophoretransport zugeschrieben werden, jedoch zeigten Mutanten der einzelnen Gene spezifische phänotypische Eigenschaften. Die tonB1-Mutante stach hervor durch ein vergleichsweise stark verzögertes Wachstum unter diazotrophen Bedingungen. Es konnte gezeigt werden, dass sowohl die Nitrogenaseaktivität als auch die expression vermindert war im tonB1-Mutantenstamm. Außerdem zeigten die Heterozysten dieser Mutante, die auf die Stickstoffixierung spezialisierten Zellen, eine abnormale Morphologie. Da die Expression von tonB1 jedoch nach dem Überführen von Wildypzellen in stickstoffreies Medium nicht erhöht war, kann eine direkte Beteiligung von TonB1 an der Heterozystendifferenzierung als unwahrscheinlich betrachtet werden. Die Zelleinschnürungen zwischen Heterozysten und vegetativen Zellen waren in I-tonB1 weniger ausgeprägt als im Wildtyp, was durch eine Anfärbung der Zellwand mit einem Fluoreszenzmarker gezeigt werden konnte. Ebenfalls konnte anhand des fluoreszierenden Markers Calcein gezeigt werden, dass die molekulare Diffusionsgeschwindigkeit zwischen Heterozysten und vegetativen Zellen, und auch zwischen zwei benachbarten vegetativen Zellen, in der tonB1-Mutante erhöht ist. Deswegen kann hier vermutlich vermehrt die Nitrogenase schädigender Sauerstoff in Heterozysten eindringen. Die aufgezählten Ergebnisse deuten auf eine Funktion von SjdR im Aufbau der Septumsstrukturen hin, beispielsweise durch Regulation der Peptidoglykansynthese oder -verteilung, weswegen TonB1 umbenannt wurde in SjdR (Septal junction disc regulator).
Die Untersuchung der tonB2-Mutante zeigte bei dieser eine veränderte Pigmentierung, eine vermehrte Lipopolysaccharidproduktion und Filamentaggregation sowie eine erhöhte Resistenz gegenüber bestimmten Antibiotika oder Detergenzien. Letzteres könnte auf die ebenfalls in der tonB2-Mutante beobachtete verringerte Porinexpression zurückgeführt werden. Es wurde außerdem eine vermehrte Anreicherung von Kupfer und Molybdän in der Mutante gemessen, was ein Grund für die Veränderte Pigmentierung sein könnte und ebenfalls die Porinexpression beeinflussen könnte. Insgesamt scheint sich das Fehlen von TonB2 auf die Integrität der Äußeren Membran auszuwirken. Daher kann für TonB2, eine Funktion in Anlehnung an das Tol-system vermutet werden.
Cerumen was found to be a promising alternative specimen for the detection of drugs. In a pilot study, drugs of abuse were identified at a higher detection rate and a longer detection window in cerumen than in urine. In this study, cerumen from subjects was analyzed after they ingested the designer stimulant 4-fluoroamphetamine (4-FA) in a controlled manner. Methods: Twelve subjects ingested placebo and 100 mg of 4-FA. Five of them were also given 150 mg of 4-FA in 150 mL Royal Club bitter lemon drink at least after 7 days. Cerumen was sampled using cotton swabs at baseline, 1 h after the ingestion of the drug and at the end of the study day (12 h). After extraction with ethyl acetate followed by solid-phase extraction, the extracts were analyzed using liquid chromatography coupled with tandem mass spectrometry (LC–MS/MS). Results and discussion: In the cerumen of all 12 subjects, 4-FA was detected 12 h after its ingestion; in most subjects, cerumen was detected after 1 h of ingestion, ranging from 0.06 to 13.90 (median 1.52) ng per swab. The detection of 4-FA in cerumen sampled 7 days or more after the first dose suggested a long detection window of cerumen. Conclusions: Cerumen can be successfully used to detect a single drug ingestion even immediately after the ingestion when a sufficient amount of cerumen is used.
One of the most challenging problems in solid state systems is the microscopic analysis of electronic correlations. A paramount minimal model that encodes correlation effects is the Hubbard Hamiltonian, which—regardless of its simplicity—is exactly solvable only in a few limiting cases and approximate many-body methods are required for its solution. In this review, an overview on the non-perturbative two-particle self-consistent method (TPSC), which was originally introduced to describe the electronic properties of the single-band Hubbard model, is presented. A detailed derivation of the multi-orbital generalization of TPSC is introduced here and particular features of the method on exemplary interacting models in comparison to dynamical mean-field theory results are discussed.
Super-resolution optical fluctuation imaging (SOFI) is a super-resolution microscopy technique that overcomes the diffraction limit by analyzing intensity fluctuations of statistically independent emitters in a time series of images. The final images are background-free and show confocality and enhanced spatial resolution (super-resolution). Fluorophore photobleaching, however, is a key limitation for recording long time series of images that will allow for the calculation of higher order SOFI results with correspondingly increased resolution. Here, we demonstrate that photobleaching can be circumvented by using fluorophore labels that reversibly and transiently bind to a target, and which are being replenished from a buffer which serves as a reservoir. Using fluorophore-labeled short DNA oligonucleotides, we labeled cellular structures with target-specific antibodies that contain complementary DNA sequences and record the fluctuation events caused by transient emitter binding. We show that this concept bypasses extensive photobleaching and facilitates two-color imaging of cellular structures with SOFI.
Designed multitarget ligands are a popular approach to generating efficient and safe drugs, and fragment-based strategies have been postulated as a versatile avenue to discover multitarget ligand leads. To systematically probe the potential of fragment-based multiple ligand discovery, we have employed a large fragment library for comprehensive screening on five targets chosen from proteins for which multitarget ligands have been successfully developed previously (soluble epoxide hydrolase, leukotriene A4 hydrolase, 5-lipoxygenase, retinoid X receptor, farnesoid X receptor). Differential scanning fluorimetry served as primary screening method before fragments hitting at least two targets were validated in orthogonal assays. Thereby, we obtained valuable fragment leads with dual-target engagement for six out of ten target combinations. Our results demonstrate the applicability of fragment-based approaches to identify starting points for polypharmacological compound development with certain limitations.
Background: The approval of everolimus (EVE) for the treatment of angiomyolipoma (2013), subependymal giant cell astrocytoma (2013) and drug-refractory epilepsy (2017) in patients with tuberous sclerosis complex (TSC) represents the first disease-modifying treatment option available for this rare and complex genetic disorder. Objective: The objective of this study was to analyse the use, efficacy, tolerability and treatment retention of EVE in patients with TSC in Germany from the patient’s perspective. Methods: A structured cross-age survey was conducted at 26 specialised TSC centres in Germany and by the German TSC patient advocacy group between February and July 2019, enrolling children, adolescents and adult patients with TSC. Results: Of 365 participants, 36.7% (n = 134) reported the current or past intake of EVE, including 31.5% (n = 115) who were taking EVE at study entry. The mean EVE dosage was 6.1 ± 2.9 mg/m2 (median: 5.6 mg/m2, range 2.0–15.1 mg/m2) in children and adolescents and 4 ± 2.1 mg/m2 (median: 3.7 mg/m2, range 0.8–10.1 mg/m2) in adult patients. An early diagnosis of TSC, the presence of angiomyolipoma, drug-refractory epilepsy, neuropsychiatric manifestations, subependymal giant cell astrocytoma, cardiac rhabdomyoma and overall multi-organ involvement were associated with the use of EVE as a disease-modifying treatment. The reported efficacy was 64.0% for angiomyolipoma (75% in adult patients), 66.2% for drug-refractory epilepsy, and 54.4% for subependymal giant cell astrocytoma. The overall retention rate for EVE was 85.8%. The retention rates after 12 months of EVE therapy were higher among adults (93.7%) than among children and adolescents (88.7%; 90.5% vs 77.4% after 24 months; 87.3% vs 77.4% after 36 months). Tolerability was acceptable, with 70.9% of patients overall reporting adverse events, including stomatitis (47.0%), acne-like rash (7.7%), increased susceptibility to common infections and lymphoedema (each 6.0%), which were the most frequently reported symptoms. With a total score of 41.7 compared with 36.8 among patients not taking EVE, patients currently being treated with EVE showed an increased Liverpool Adverse Event Profile. Noticeable deviations in the sub-items ‘tiredness’, ‘skin problems’ and ‘mouth/gum problems’, which are likely related to EVE-typical adverse effects, were more frequently reported among patients taking EVE. Conclusions: From the patients’ perspective, EVE is an effective and relatively well-tolerated disease-modifying treatment option for children, adolescents and adults with TSC, associated with a high long-term retention rate that can be individually considered for each patient. Everolimus therapy should ideally be supervised by a centre experienced in the use of mechanistic target of rapamycin inhibitors, and adverse effects should be monitored on a regular basis.
Climate change causes increased tree mortality leading to canopy loss and thus sun-exposed forest floors. Sun exposure creates extreme temperatures and radiation, with potentially more drastic effects on forest organisms than the current increase in mean temperature. Such conditions might potentially negatively affect the maturation of mushrooms of forest fungi. A failure of reaching maturation would mean no sexual spore release and, thus, entail a loss of genetic diversity. However, we currently have a limited understanding of the quality and quantity of mushroom-specific molecular responses caused by sun exposure. Thus, to understand the short-term responses toward enhanced sun exposure, we exposed mushrooms of the wood-inhabiting forest species Lentinula edodes, while still attached to their mycelium and substrate, to artificial solar light (ca. 30°C and 100,000 lux) for 5, 30, and 60 min. We found significant differentially expressed genes at 30 and 60 min. Eukaryotic Orthologous Groups (KOG) class enrichment pointed to defense mechanisms. The 20 most significant differentially expressed genes showed the expression of heat-shock proteins, an important family of proteins under heat stress. Although preliminary, our results suggest mushroom-specific molecular responses to tolerate enhanced sun exposure as expected under climate change. Whether mushroom-specific molecular responses are able to maintain fungal fitness under opening forest canopies remains to be tested.
Our purpose was to analyze the robustness and reproducibility of magnetic resonance imaging (MRI) radiomic features. We constructed a multi-object fruit phantom to perform MRI acquisition as scan-rescan using a 3 Tesla MRI scanner. We applied T2-weighted (T2w) half-Fourier acquisition single-shot turbo spin-echo (HASTE), T2w turbo spin-echo (TSE), T2w fluid-attenuated inversion recovery (FLAIR), T2 map and T1-weighted (T1w) TSE. Images were resampled to isotropic voxels. Fruits were segmented. The workflow was repeated by a second reader and the first reader after a pause of one month. We applied PyRadiomics to extract 107 radiomic features per fruit and sequence from seven feature classes. We calculated concordance correlation coefficients (CCC) and dynamic range (DR) to obtain measurements of feature robustness. Intraclass correlation coefficient (ICC) was calculated to assess intra- and inter-observer reproducibility. We calculated Gini scores to test the pairwise discriminative power specific for the features and MRI sequences. We depict Bland Altmann plots of features with top discriminative power (Mann–Whitney U test). Shape features were the most robust feature class. T2 map was the most robust imaging technique (robust features (rf), n = 84). HASTE sequence led to the least amount of rf (n = 20). Intra-observer ICC was excellent (≥ 0.75) for nearly all features (max–min; 99.1–97.2%). Deterioration of ICC values was seen in the inter-observer analyses (max–min; 88.7–81.1%). Complete robustness across all sequences was found for 8 features. Shape features and T2 map yielded the highest pairwise discriminative performance. Radiomics validity depends on the MRI sequence and feature class. T2 map seems to be the most promising imaging technique with the highest feature robustness, high intra-/inter-observer reproducibility and most promising discriminative power.
Lack of efficacy of a partial adenosine A1 receptor agonist in neuropathic pain models in mice
(2021)
Previous studies suggest that adenosine A1 receptors (A1R) modulate the processing of pain. The aim of this study was to characterize the distribution of A1R in nociceptive tissues and to evaluate whether targeting A1R with the partial agonist capadenoson may reduce neuropathic pain in mice. The cellular distribution of A1R in dorsal root ganglia (DRG) and the spinal cord was analyzed using fluorescent in situ hybridization. In behavioral experiments, neuropathic pain was induced by spared nerve injury or intraperitoneal injection of paclitaxel, and tactile hypersensitivities were determined using a dynamic plantar aesthesiometer. Whole-cell patch-clamp recordings were performed to assess electrophysiological properties of dissociated DRG neurons. We found A1R to be expressed in populations of DRG neurons and dorsal horn neurons involved in the processing of pain. However, administration of capadenoson at established in vivo doses (0.03–1.0 mg/kg) did not alter mechanical hypersensitivity in the spared nerve injury and paclitaxel models of neuropathic pain, whereas the standard analgesic pregabalin significantly inhibited the pain behavior. Moreover, capadenoson failed to affect potassium currents in DRG neurons, in contrast to a full A1R agonist. Despite expression of A1R in nociceptive neurons, our data do not support the hypothesis that pharmacological intervention with partial A1R agonists might be a valuable approach for the treatment of neuropathic pain.
Patients with ataxia-telangiectasia (A-T) suffer from progressive cerebellar ataxia, immunodeficiency, respiratory failure, and cancer susceptibility. From a clinical point of view, A-T patients with IgA deficiency show more symptoms and may have a poorer prognosis. In this study, we analyzed mortality and immunity data of 659 A-T patients with regard to IgA deficiency collected from the European Society for Immunodeficiencies (ESID) registry and from 66 patients with classical A-T who attended at the Frankfurt Goethe-University between 2012 and 2018. We studied peripheral B- and T-cell subsets and T-cell repertoire of the Frankfurt cohort and survival rates of all A-T patients in the ESID registry. Patients with A-T have significant alterations in their lymphocyte phenotypes. All subsets (CD3, CD4, CD8, CD19, CD4/CD45RA, and CD8/CD45RA) were significantly diminished compared to standard values. Patients with IgA deficiency (n = 35) had significantly lower lymphocyte counts compared to A-T patients without IgA deficiency (n = 31) due to a further decrease of naïve CD4 T-cells, central memory CD4 cells, and regulatory T-cells. Although both patient groups showed affected TCR-ß repertoires compared to controls, no differences could be detected between patients with and without IgA deficiency. Overall survival of patients with IgA deficiency was significantly diminished. For the first time, our data show that patients with IgA deficiency have significantly lower lymphocyte counts and subsets, which are accompanied with reduced survival, compared to A-T patients without IgA deficiency. IgA, a simple surrogate marker, is indicating the poorest prognosis for classical A-T patients. Both non-interventional clinical trials were registered at clinicaltrials.gov 2012 (Susceptibility to infections in ataxia-telangiectasia; NCT02345135) and 2017 (Susceptibility to Infections, tumor risk and liver disease in patients with ataxia-telangiectasia; NCT03357978)
Physical inactivity is discussed as one of the most detrimental influences for lifestyle-related medical complications such as obesity, heart disease, hypertension, diabetes and premature mortality in in- and outpatients with major depressive disorder (MDD). In contrast, intervention studies indicate that moderate-to-vigorous-intensity physical activity (MVPA) might reduce complications and depression symptoms itself. Self-reported data on depression [Beck-Depression-Inventory-II (BDI-II)], general habitual well-being (FAHW), self-esteem and physical self-perception (FAHW, MSWS) were administrated in a cross-sectional study with 76 in- and outpatients with MDD. MVPA was documented using ActiGraph wGT3X + ® accelerometers and fitness was measured using cardiopulmonary exercise testing (CPET). Subgroups were built according to activity level (low PA defined as MVPA < 30 min/day, moderate PA defined as MVPA 30–45 min/day, high PA defined as MVPA > 45 min/day). Statistical analysis was performed using a Mann–Whitney U and Kruskal–Wallis test, Spearman correlation and mediation analysis. BDI-II scores and MVPA values of in- and outpatients were comparable, but fitness differed between the two groups. Analysis of the outpatient group showed a negative correlation between BDI-II and MVPA. No association of inpatient MVPA and psychopathology was found. General habitual well-being and self-esteem mediated the relationship between outpatient MVPA and BDI-II. The level of depression determined by the BDI-II score was significantly higher in the outpatient low- and moderate PA subgroups compared to outpatients with high PA. Fitness showed no association to depression symptoms or well-being. To ameliorate depressive symptoms of MDD outpatients, intervention strategies should promote habitual MVPA and exercise exceeding the duration recommended for general health (≥ 30 min/day). Further studies need to investigate sufficient MVPA strategies to impact MDD symptoms in inpatient settings. Exercise effects seem to be driven by changes of well-being rather than increased physical fitness.
An investigation of photoelectron angular distributions and circular dichroism of chiral molecules
(2021)
The present work demonstrates the capability of several type of molecular frame photoelectron angular distributions (MFPADs) and their linked chiroptical phenomenon the photoelectron circular dichroism (PECD) to map in great detail the molecular geometry of polyatomic chiral molecules as a function of photoelectron energy. To investigate the influence of the molecular potential on the MFPADs, two chiral molecules were selected, namely 2-(methyl)oxirane (C3H6O, MOx, m = 58,08 uma) and 2-(trifluoromethyl)oxirane (C3H3F3O, TFMOx, m = 112,03 uma). The two molecules differs in one substitutional group and share an oxirane group where the O(1s) electron was directly photoionized with the use of synchrotron radiation in the soft X-ray regime. The direct photoionization of the K-shell electron is well localized in the molecule and it induces the ejection of two or more electrons; the excited system separates into several charged (and eventually neutral) fragments which undergo Coulomb explosion due to their charges. The electrons and the fragments were detected using the COLd Target Recoil Ion Momentum Spectroscopy (COLTRIMS) and the momentum vectors calculated for each fragment belonging from a single ionization. The former method gives the possibility to post-orient molecules in space, giving access to the molecular frame, thus the MFPAD and its related PECD for multiple light propagation direction.
Stereochemistry (from the Greek στερεο- stereo- meaning solid) refers to chemistry in three dimensions. Since most molecules show a three-dimensional structure (3D), stereochemistry pervades all fields of chemistry and biology, and it is an essential point of view for the understanding of chemical structure, molecular dynamics and molecular reactions. The understanding of the chemistry of life is tightly bounded with major discoveries in stereochemistry, which triggered tremendous technical advancements, making it a flourishing field of research since its revolutionary introduction in late 18th century. In chemistry, chirality is a brunch of stereochemistry which focuses on objects with the peculiar geometrical property of not being superimposable to their mirror-images. The word chirality is derived from the Greek χειρ for “hand”, and the first use of this term in chemistry is usually attributed to Lord Kelvin who called during a lecture at the Oxford University Junior Scientific Club in 1893 “any geometrical figure, or group of points, “chiral”, and say that it has chirality if its image in a plane mirror, ideally realized, cannot be brought to coincide with itself.”. Although the latter is usually considered as the birth of the word chirality, the concept underlying it was already present in several fields of science (above all mathematics), already proving the already multidisciplinary relevance of chirality across many field of science and beyond. Nature shows great examples of chiral symmetry on all scales. Empirically, it is possible to observe it at macroscopic scale (e.g. distribution of rotations of galaxies), down to the microscopic scale (e.g. structure of some plankton species), but it is at the molecular level where the number gets remarkable: most of the pharmaceutical drugs, food fragrances, pheromones, enzymes, amino acids and DNA molecules, in fact, are chiral. Moreover, the concept of chirality goes far beyond the mere spatial symmetry of objects being crucially entangled with the fundamental properties of physical forces in nature. The symmetry breaking, namely the different physical behaviour of a two chiral systems upon the same stimuli, is considered to be one of the best explanation for the long standing questions of homochirality in biological life, and ultimately to the chemical origin of life on Earth as we know it. Our organism shows high enantio-selectivity towards specific compounds ranging from drugs, to fragrances. Over 800 odour molecules commonly used in food and fragrance industries have been identified as chiral and their enantiomeric forms are perceived to have very different smells, as the well-know example of D- and L- limonene. Similarly, responses to pharmaceuticals drugs can be enantiomer specific, and in fact about 60 % the drugs currently on the market are chiral compounds, and nearly 90 % of them are sold as racemates. The same degree of enantio-selectivity is observed in the communications systems of plants and insects. Plants produce lipophilic liquids with high vapour pressure called plant volatiles (PVs) which are synthesized via different enzymes called tarpene synthases that are usually chiral. Chiral molecules and chiral effects have a strong impact on all the fields of science with exciting developments ranging from stereo-selective synthesis based on heterogeneous enantioselective catalysis, to optoelctronics, to photochemical asymmetric synthesis, and chiral surface science, just to cite a few.
Chiral molecules come in two forms called enantiomers. Their almost identical chemical and physical properties continue to pose technical challenges concerning the resolution of racemic mixtures, the determination of the enantiomeric excess, and the direct determination of the absolute configuration of an enantiomer. ...
This work is about resumptive and non-resumptive relative clauses (RCs) in the three big Ibero-Romance languages: Spanish, Portuguese, and Catalan. In (1), the examined structures are exemplified for Spanish: (1a.) No conozco el hombre que viste _ ayer. “I don’t know the man that you saw yesterday.” (1b.) Es este el hombre que le enviaron el libro. “This is the man to whom they sent the book.” (1c.) Es este el hombre a quien le enviaron el libro. “This is the man to whom they sent the book.”
(1a.) displays a non-resumptive, or canonical, RC, which is characterized by the canonical use of a relativizing operator and a gap in the subordinate’s object position, a piece of evidence which has induced most of the generative literature to assume wh-movement of the relative operator in the sense of Chomsky (1977). The last two decades, however, have seen a big debate regarding the exact derivational analysis, starting with Kayne’s (1994) antisymmetry theory and the following focus on reconstruction and anti-reconstruction effects in RCs. This search for the correct starting site of the RC’s head noun has dismissed the original Head External Analysis (HEA) (Chomsky 1965, 1977) and led to the development of a Head Raising Analysis (RA) (Kayne 1994, Bianchi 1999, a.o.) and a Matching Analysis (MA) (Munn 1994, Sauerland 1998, a.o.). The discussion in this work argues that the data on reconstruction and anti-reconstruction effects are not sufficiently clear and reliable in order to adopt one of the head-internal analyses, i.e. a HEA or a MA. Instead, the work follows a variant of the HEA proposed for Portuguese by Rinke & Aßmann (2017), which adheres to standard assumptions about Romance syntax, and avoids the empirical problems that the other proposals have to face. Arguing that the HEA holds for all Ibero-Romance languages, this work also takes a stance in the debate around the categorical status of the relativizing element que and argues that it is always a D-element, and never of category C, i.e. there is no such thing as a relativizing complementizer (cf. also Kayne 2010, Kato & Nunes 2008, Poletto & Sanfelici 2018).
The work argues that wh-movement in a HEA fashion is the correct analysis also for resumptive relative clauses as in (1b., c.), which crucially lack a gap in argument position but show a resumptive pronominal element instead. Furthermore, it takes advantage of the fact that the choice of such genetically closely related languages like Spanish, Portuguese, and Catalan enables research to address the phenomenon under consideration from a microcomparative perspective, which is “the closest we can come … to a controlled experiment in comparative syntax” (Kayne 2005: 281-282). The descriptive literature suggests that, at least for Spanish and Catalan, there are two types of a resumptive RC structure available: a simple resumption as in (1b.), including mere que, and a complex resumption structure which displays a more complex relativizer like a quien in combination with a resumptive pronoun (1c.). However, a corpus study carried out for this work reveals that speakers of the three languages behave alike insofar as the only resumptive RC used in spontaneous speech is a simple-resumption structure, while complex resumption never occurs. Additionally, a multivariate analysis shows that in all three languages, grammatical case is the most important factor when it comes to the possibility of a resumptive structure in RCs: with a dative argument, simple resumption is obligatory, while for accusative and nominative arguments, resumption is optional. The discussion concludes that simple and complex resumption constitute different phenomena also on a structural level: the latter one is argued to be a subcase of clitic doubling, and therefore, receives an analysis along the lines of Pineda (2016), who argues against a dative alternation in Romance languages and locates the (non-)realisation of the dative clitic in a transitive clitic-doubling structure outside of syntax, it being a case of silent variation along the lines of Sigurðsson (2004) and Kayne (2005). From this perspective, it follows naturally that in Portuguese, complex resumption structures are ungrammatical. Simple resumption, on the other hand, which is a possible structure in all three languages, is argued to represent the phonological counterpart of “scattered deletion”, i.e. the preferred interpretation for an A’-chain according to Chomsky (2003): in the operator position SpecCP, every feature except for the operator feature is deleted, resulting in the phonological outcome que, while in the variable position, everything but the operator is interpreted, resulting in a pronominal element according to the argument’s phi-features.
This work takes a stance in the latest topics on generative analyses for relative clauses. Using not only theoretical considerations but conclusions drawn from empirical data on three languages, it offers a new perspective on pending questions and proposes to take a fresh look on supposedly outdated analyses.
This article investigates the roles of psychological biases for deviations between subjective survival beliefs (SSBs) and objective survival probabilities. We model these deviations through age-dependent inverse S-shaped probability weighting functions. Our estimates suggest that implied measures for cognitive weakness increase and relative optimism decrease with age. Direct measures of cognitive weakness and optimism share these trends. Our regression analyses confirm that these factors play strong quantitative roles in the formation of SSBs. Our main finding is that cognitive weakness instead of optimism becomes with age an increasingly important contributor to the well-documented overestimation of survival chances in old age.
The bacteriophage ΦX174 causes large pore formation in Escherichia coli and related bacteria. Lysis is mediated by the small membrane-bound toxin ΦX174-E, which is composed of a transmembrane domain and a soluble domain. The toxin requires activation by the bacterial chaperone SlyD and inhibits the cell wall precursor forming enzyme MraY. Bacterial cell wall biosynthesis is an important target for antibiotics; therefore, knowledge of molecular details in the ΦX174-E lysis pathway could help to identify new mechanisms and sites of action. In this study, cell-free expression and nanoparticle technology were combined to avoid toxic effects upon ΦX174-E synthesis, resulting in the efficient production of a functional full-length toxin and engineered derivatives. Pre-assembled nanodiscs were used to study ΦX174-E function in defined lipid environments and to analyze its membrane insertion mechanisms. The conformation of the soluble domain of ΦX174-E was identified as a central trigger for membrane insertion, as well as for the oligomeric assembly of the toxin. Stable complex formation of the soluble domain with SlyD is essential to keep nascent ΦX174-E in a conformation competent for membrane insertion. Once inserted into the membrane, ΦX174-E assembles into high-order complexes via its transmembrane domain and oligomerization depends on the presence of an essential proline residue at position 21. The data presented here support a model where an initial contact of the nascent ΦX174-E transmembrane domain with the peptidyl-prolyl isomerase domain of SlyD is essential to allow a subsequent stable interaction of SlyD with the ΦX174-E soluble domain for the generation of a membrane insertion competent toxin.
Certain electron-rich 1,4-diborabenzene derivatives efficiently activate single, double, and triple bonds and thereby increasingly compete with transition metals in homogeneous catalysis. This review compares the activation of three model substrates (H2, H2C=CH2, CO2) by (i) 9,10-dihydro-9,10-diboraanthracene dianions, (ii) their neutral carbene-stabilized congeners, (iii) 1,3,2,5-diazadiborinines, and (iv) 1,4,2,5-diazadiborinines. Distinct structure-properties relationships become apparent, the most influential factors being (i) the steric demands of the B-bonded substituents, (ii) the charges on the B-doped (hetero)arenes, (iii) charge polarization as a result of additional N-doping, and (iv) the energies and nodal structures of the frontier orbitals. The observed reactions are explained by a transition metal-like activation mechanism. If the two boron atoms are chemically inequivalent, contributions of a B(+I)/B(+III) mixed-valence state determine the observed regioselectivities when polar substrates are added. The lessons learned from the conversions of the model substrates are subsequently used to rationalize the behavior of the B2 heterocycles also toward more sophisticated substrate molecules. Finally, catalytic cycles based on H2- and H−-transfers, hydroboration reactions, and CO2 reductions will be covered.
Background: Approximately one in three patients suffers from preoperative anaemia. Even though haemoglobin is measured before surgery, anaemia management is not implemented in every hospital. Objective: Here, we demonstrate the implementation of an anaemia walk-in clinic at an Orthopedic University Hospital. To improve the diagnosis of iron deficiency (ID), we examined whether reticulocyte haemoglobin (Ret-He) could be a useful additional parameter. Material and Methods: In August 2019, an anaemia walk-in clinic was established. Between September and December 2019, major orthopaedic surgical patients were screened for preoperative anaemia. The primary endpoint was the incidence of preoperative anaemia. Secondary endpoints included Ret-He level, red blood cell (RBC) transfusion rate, in-hospital length of stay and anaemia at hospital discharge. Results: A total of 104 patients were screened for anaemia. Preoperative anaemia rate was 20.6%. Intravenous iron was supplemented in 23 patients. Transfusion of RBC units per patient (1.7 ± 1.2 vs. 0.2 ± 0.9; p = 0.004) and hospital length of stay (13.1 ± 4.8 days vs. 10.6 ± 5.1 days; p = 0.068) was increased in anaemic patients compared to non-anaemic patients. Ret-He values were significantly lower in patients with ID anaemia (33.3 pg [28.6–40.2 pg]) compared to patients with ID (35.3 pg [28.9–38.6 pg]; p = 0.015) or patients without anaemia (35.4 pg [30.2–39.4 pg]; p = 0.001). Conclusion: Preoperative anaemia is common in orthopaedic patients. Our results proved the feasibility of an anaemia walk-in clinic to manage preoperative anaemia. Furthermore, our analysis supports the use of Ret-He as an additional parameter for the diagnosis of ID in surgical patients.
USP22 controls necroptosis by regulating receptor-interacting protein kinase 3 ubiquitination
(2020)
Dynamic control of ubiquitination by deubiquitinating enzymes is essential for almost all biological processes. Ubiquitin-specific peptidase 22 (USP22) is part of the SAGA complex and catalyzes the removal of mono-ubiquitination from histones H2A and H2B, thereby regulating gene transcription. However, novel roles for USP22 have emerged recently, such as tumor development and cell death. Apart from apoptosis, the relevance of USP22 in other programmed cell death pathways still remains unclear. Here, we describe a novel role for USP22 in controlling necroptotic cell death in human tumor cell lines. Loss of USP22 expression significantly delays TNFα/Smac mimetic/zVAD.fmk (TBZ)-induced necroptosis, without affecting TNFα-mediated NF-κB activation or extrinsic apoptosis. Ubiquitin remnant profiling identified receptor-interacting protein kinase 3 (RIPK3) lysines 42, 351, and 518 as novel, USP22-regulated ubiquitination sites during necroptosis. Importantly, mutation of RIPK3 K518 reduced necroptosis-associated RIPK3 ubiquitination and amplified necrosome formation and necroptotic cell death. In conclusion, we identify a novel role of USP22 in necroptosis and further elucidate the relevance of RIPK3 ubiquitination as crucial regulator of necroptotic cell death.
In situ investigation of membrane proteins is a challenging task. Previously we demonstrated that nitroxide labels combined with pulsed ESR spectroscopy is a promising tool for this purpose. However, the nitroxide labels suffer from poor stability, high background labeling, and low sensitivity. Here we show that Finland (FTAM) and OX063 based labels enable labeling of the cobalamin transporter BtuB and BamA, the central component of the β-barrel assembly machinery (BAM) complex, in E coli. Compared to the methanethiosulfonate spin label (MTSL), trityl labels eliminated the background signals and enabled specific in situ labeling of the proteins with high efficiency. The OX063 labels show a long phase memory time (TM) of ≈5 μs. All the trityls enabled distance measurements between BtuB and an orthogonally labeled substrate with high selectivity and sensitivity down to a few μm concentration. Our data corroborate the BtuB and BamA conformations in the cellular environment of E. coli.
Background and purpose: Superficial siderosis of the central nervous system is a sporadic finding in magnetic resonance imaging, resulting from recurrent bleedings into the subarachnoid space. This study aimed to determine the frequency of spinal dural cerebrospinal fluid (CSF) leaks amongst patients with a symmetric infratentorial siderosis pattern. Methods: In all, 97,733 magnetic resonance images performed between 2007 and 2018 in our neurocenter were screened by a keyword search for “hemosiderosis” and “superficial siderosis.” Siderosis patterns on brain imaging were classified according to a previously published algorithm. Potential causative intracranial bleeding events were also assessed. Patients with a symmetric infratentorial siderosis pattern but without causative intracranial bleeding events in history were prospectively evaluated for spinal pathologies. Results: Forty-two patients with isolated supratentorial siderosis, 30 with symmetric infratentorial siderosis and 21 with limited (non-symmetric) infratentorial siderosis were identified. Amyloid angiopathy and subarachnoid hemorrhage were causes for isolated supratentorial siderosis. In all four patients with a symmetric infratentorial siderosis pattern but without a causative intracranial bleeding event in history, spinal dural abnormalities were detected. Dural leaks were searched for in patients with symmetric infratentorial siderosis and a history of intracranial bleeding event without known bleeding etiology, considering that spinal dural CSF leaks themselves may also cause intracranial hemorrhage, for example by inducing venous thrombosis due to low CSF pressure. Thereby, one additional spinal dural leak was detected. Conclusions: Persisting spinal dural CSF leaks can frequently be identified in patients with a symmetric infratentorial siderosis pattern. Diagnostic workup in these cases should include magnetic resonance imaging of the whole spine.
Autophagy is a highly conserved catabolic process cells use to maintain their homeostasis by degrading misfolded, damaged and excessive proteins, nonfunctional organelles, foreign pathogens and other cellular components. Hence, autophagy can be nonselective, where bulky portions of the cytoplasm are degraded upon stress, or a highly selective process, where preselected cellular components are degraded. To distinguish between different cellular components, autophagy employs selective autophagy receptors, which will link the cargo to the autophagy machinery, thereby sequestering it in the autophagosome for its subsequent degradation in the lysosome. Autophagy receptors undergo post-translational and structural modifications to fulfil their role in autophagy, or upon executing their role, for their own degradation. We highlight the four most prominent protein modifications – phosphorylation, ubiquitination, acetylation and oligomerisation – that are essential for autophagy receptor recruitment, function and turnover. Understanding the regulation of selective autophagy receptors will provide deeper insights into the pathway and open up potential therapeutic avenues.
Linking epigenetic signature and metabolic phenotype in IDH mutant and IDH wildtype diffuse glioma
(2020)
Aims: Changes in metabolism are known to contribute to tumour phenotypes. If and how metabolic alterations in brain tumours contribute to patient outcome is still poorly understood. Epigenetics impact metabolism and mitochondrial function. The aim of this study is a characterisation of metabolic features in molecular subgroups of isocitrate dehydrogenase mutant (IDHmut) and isocitrate dehydrogenase wildtype (IDHwt) gliomas. Methods: We employed DNA methylation pattern analyses with a special focus on metabolic genes, large-scale metabolism panel immunohistochemistry (IHC), qPCR-based determination of mitochondrial DNA copy number and immune cell content using IHC and deconvolution of DNA methylation data. We analysed molecularly characterised gliomas (n = 57) for in depth DNA methylation, a cohort of primary and recurrent gliomas (n = 22) for mitochondrial copy number and validated these results in a large glioma cohort (n = 293). Finally, we investigated the potential of metabolic markers in Bevacizumab (Bev)-treated gliomas (n = 29). Results: DNA methylation patterns of metabolic genes successfully distinguished the molecular subtypes of IDHmut and IDHwt gliomas. Promoter methylation of lactate dehydrogenase A negatively correlated with protein expression and was associated with IDHmut gliomas. Mitochondrial DNA copy number was increased in IDHmut tumours and did not change in recurrent tumours. Hierarchical clustering based on metabolism panel IHC revealed distinct subclasses of IDHmut and IDHwt gliomas with an impact on patient outcome. Further quantification of these markers allowed for the prediction of survival under anti-angiogenic therapy. Conclusion: A mitochondrial signature was associated with increased survival in all analyses, which could indicate tumour subgroups with specific metabolic vulnerabilities.
Culturally adapted cognitive behavioral therapy (CA-CBT) is a well-evaluated, transdiagnostic group intervention for refugees that uses psychoeducation, meditation, and stretching exercises. In the current study, we added problem-solving training to CA-CBT and evaluated this treatment (i.e., CA-CBT+) in a randomized controlled pilot trial with a sample of Farsi-speaking refugees. Participants (N = 24) were male refugees diagnosed with DSM-5 PTSD, major depressive disorder, and anxiety disorders who were randomly assigned to either a treatment or waitlist control (WLC) condition. Treatment components were adapted both to the specific cultural background and the current social problems of asylum seekers. Assessments were performed pretreatment, 12-weeks posttreatment, and 1-year follow-up. The primary treatment outcome was the General Health Questionnaire (GHQ-28); secondary outcome measures included the Posttraumatic Stress Disorder Checklist, Patient Health Questionnaire, Somatic Symptom Scale, World Health Organization Quality of Life, and Emotion Regulation Scale. Eleven of 12 participants were randomized to CA-CBT+ completed treatment. Based on intent-to-treat data, large between-group effect sizes were seen at posttreatment in the GHQ-28, d = 3.0, and for most secondary outcome measures. Improvements for individuals in the treatment group decreased at 1-year follow-up, but effect sizes demonstrated continued large improvements on all measures as compared to pretreatment levels. In summary, CA-CBT+ led to large improvements in general psychopathological distress and quality of life, which were maintained in the long term. In addition, the dropout rate was very low, with delivery in group format. Thus, problem-solving training appears to be a promising addition to CA-CBT.