Geomorphological control on boulder transport and coastal erosion before, during and after an extreme extra-tropical cyclone

Extreme wave events in coastal zones are principal drivers of geomorphic change. Evidence of boulder entrainment and erosional impact during storms is increasing. However, there is currently poor time coupling between pre- and post-storm measurements of coastal boulder deposits. Importantly there are no data reporting shore platform erosion, boulder entrainment and/or boulder transport during storm events – rock coast dynamics during storm events are currently unexplored. Here, we use high-resolution (daily) field data to measure and characterise coastal boulder transport before, during and after the extreme Northeast Atlantic extra-tropical cyclone Johanna in March 2008. Forty-eight limestone fine-medium boulders (n = 46) and coarse cobbles (n = 2) were tracked daily over a 0.1 km2 intertidal area during this multi-day storm. Boulders were repeatedly entrained, transported and deposited, and in some cases broken down (n = 1) or quarried (n = 3), during the most intense days of the storm. Eighty-one percent (n = 39) of boulders were located at both the start and end of the storm. Of these, 92% were entrained where entrainment patterns were closely aligned to wave parameters. These data firmly demonstrate rock coasts are dynamic and vulnerable under storm conditions. No statistically significant relationship was found between boulder size (mass) and net transport distance. Graphical analyses suggest that boulder size limits the maximum longshore transport distance but that for the majority of boulders lying under this threshold, other factors influence transport distance. Paired analysis of 20 similar sized and shaped boulders in different morphogenic zones demonstrates that geomorphological control affects entrainment and transport distance – where net transport distances were up to 39 times less where geomorphological control was greatest. These results have important implications for understanding and for accurately measuring and modelling boulde

First lipid residue analysis of Early Neolithic pottery from Swifterbant (the Netherlands, ca. 4300–4000 BC)

This paper focuses on the functional analysis of Swifterbant pottery from North-western Europe (ca. 4300–4000 BC) through lipid residue analysis. The main aim is to understand the role of pottery in terms of its relation to hunter-fisher-gatherer lifestyle, and the change in available food resources brought about by the arrival of domesticated animal and plant products. We conducted lipid residue analysis of 62 samples from three Swifterbant sites S2, S3 and S4. A combined approach using both GC-MS and GC-C-IRMS of residues absorbed into the ceramic was employed to identify their context. Our results demonstrate that Swifterbant ceramics were used exclusively for processing aquatic resources. We also found no evidence of inter-site variation in the use of pottery or variation based on both typological and technological features of the pottery. We found no evidence for any domesticated resources despite their presence in the faunal and botanical assemblages

A Transcriptomic Severity Classifier IMX-SEV-3b to Predict Mortality in Intensive Care Unit Patients with COVID-19:A Prospective Observational Pilot Study

The prediction of disease outcomes in COVID-19 patients in the ICU is of critical importance, and the examination of host gene expressions is a promising tool. The 29-host mRNA Inflam-matix-Severity-3b (IMX-SEV-3b) classifier has been reported to predict mortality in emergency department COVID-19 patients and surgical ICU patients. The accuracy of the IMX-SEV-3b in predicting mortality in COVID-19 patients admitted to the ICU is yet unknown. Our aim was to investigate the accuracy of the IMX-SEV-3b in predicting the ICU mortality of COVID-19 patients. In addition, we assessed the predictive performance of routinely measured biomarkers and the Sequential Organ Failure Assessment (SOFA) score as well. This was a prospective observational study enrolling COVID-19 patients who received mechanical ventilation on the ICU of the Erasmus MC, the Netherlands. The IMX-SEV-3b scores were generated by amplifying 29 host response genes from blood collected in PAXgene® Blood RNA tubes. A severity score was provided, ranging from 0 to 1 for increasing disease severity. The primary outcome was the accuracy of the IMX-SEV-3b in predicting ICU mortality, and we calculated the AUROC of the IMX-SEV-3b score, the biomarkers C-reactive protein (CRP), D-dimer, ferritin, leukocyte count, interleukin-6 (IL-6), lactate dehydrogenase (LDH), neutrophil-to-lymphocyte ratio (NLR), procalcitonin (PCT) and the SOFA score. A total of 53 patients were included between 1 March and 30 April 2020, with 47 of them being included within 72 h of their admission to the ICU. Of these, 18 (34%) patients died during their ICU stay, and the IMX-SEV-3b scores were significantly higher in non-survivors compared to survivors (0.65 versus 0.57, p = 0.05). The Area Under the Receiver Operating Characteristic Curve (AUROC) for prediction of ICU mortality by the IMX-SEV-3b was 0.65 (0.48–0.82). The AUROCs of the biomarkers ranged from 0.52 to 0.66, and the SOFA score had an AUROC of 0.81 (0.69–0.93). The AUROC of the pooled biomarkers CRP, D-dimer, ferritin, leukocyte count, IL-6, LDH, NLR and PCT for prediction of ICU mortality was 0.81 (IQR 0.69–0.93). Further validation in a larger interventional trial of a point-of-care version of the IMX-SEV-3b classifier is warranted to determine its value for patient management.</p

Delineating the Genetic Component of Gene Expression in Major Depression

Background: Major depression (MD) is determined by a multitude of factors including genetic risk variants that regulate gene expression. We examined the genetic component of gene expression in MD by performing a transcriptome-wide association study (TWAS), inferring gene expression–trait relationships from genetic, transcriptomic, and phenotypic information. Methods: Genes differentially expressed in depression were identified with the TWAS FUSION method, based on summary statistics from the largest genome-wide association analysis of MD (n = 135,458 cases, n = 344,901 controls) and gene expression levels from 21 tissue datasets (brain; blood; thyroid, adrenal, and pituitary glands). Follow-up analyses were performed to extensively characterize the identified associations: colocalization, conditional, and fine-mapping analyses together with TWAS-based pathway investigations. Results: Transcriptome-wide significant differences between cases and controls were found at 94 genes, approximately half of which were novel. Of the 94 significant genes, 6 represented strong, colocalized, and potentially causal associations with depression. Such high-confidence associations include NEGR1, CTC-467M3.3, TMEM106B, LRFN5, ESR2, and PROX2. Lastly, TWAS-based enrichment analysis highlighted

Transcriptional Profiling of the Caloric Restriction in Key Metabolic Tissues of Pigs Differing in Feed Efficiency

Residual feed intake is a measure of feed efficiency, where low RFI denotes high feed efficiency. Caloric restriction (CR) is associated with feed efficiency in livestock species and to human health benefits such as longevity and cancer prevention. We have developed pig lines that differ in RFI and we are interested in identifying the genes and pathways that underlie feed efficiency. Prepubertal Yorkshire gilts with low RFI (n=10) or high RFI (n=10) were fed ad libitum or at 80% of maintenance for 8 days. We measured serum metabolites and generated transcriptional profiles of liver and subcutaneous adipose tissue on these animals. Overall, 6,114 genes in fat and 305 genes in liver were differentially expressed (DE) in response to CR, and 311 genes in fat and 147 genes in liver were DE due to RFI differences. Pathway analyses of CR-induced DE genes indicated a dramatic switch to a conservation mode of energy usage by down-regulating lipogenesis and steroidogenesis in both liver and fat. Interestingly, CR altered expression of genes in immune and cell cycle/apoptotic pathways in fat, which may explain part of the CR-driven lifespan enhancement. In-silico analysis of transcription factors revealed ESR1 as a putative regulator of the adaptive response to CR, as several targets of ESR1 in our DE fat genes were annotated as cell cycle/apoptosis genes. The lipid metabolic pathway was overrepresented by down-regulated genes due to both CR and low RFI. We propose a common energy conservation mechanism, which may be controlled by PPARA, PPARG, and/or CREB in both CR and feed efficient pigs

Use of Transcriptional Profiling and Assessment of Blood Parameters to Understand Biological Mechanisms Controlling Feed Intake and Efficiency in Pigs

In this study, using transcriptional profiling of key tissues, we aimed to identify genetic mechanisms differing between control pigs and pigs that have been under selection for low residual feed intake (RFI) for three generations. A further aim was to determine the pathways responding to feed restriction within these lines and any line x treatment interactions resulting in gene expression differences. Preliminary results indicate that 2,809 genes in fat (p\u3c0.04, q\u3c0.2) and 61 genes in liver (p\u3c0.001, q\u3c0.2) showed differential expression in response to feed restriction. Also, 1,247 genes (p\u3c0.02, q\u3c0.2) showed differential expression between low RFI and control pigs and 38 genes (p\u3c0.001, q\u3c0.2) showed a line x feed interaction in liver. In addition, we measured the concentration of some of the important feed intake regulators in the blood such as leptin, triglyceride, and glucose. We found that the average blood leptin level to be significantly higher in the control ad libitum (CA) pigs than the control restricted (CR) group. Interestingly, the selected line of pigs on both restricted (SR) and ad libitum (SA) feed had similar blood leptin levels as found in the CR group pigs. Serum glucose levels were higher in CR than CA, however, we observed an opposite trend in the selected group. Combined with the transcriptional profiling results, blood hormone parameters may help us understand potential pathways that control FI and FE in pigs

Impact of disease, cognitive and behavioural factors on caregiver outcome in amyotrophic lateral sclerosis

Up to 50% of patients with amyotrophic lateral sclerosis (ALS) show mild to moderate cognitive-behavioural change alongside their progressive functional impairment. This study examines the relative impact of patients' disease symptoms, behavioural change and current executive function and social cognition abilities on psychosocial outcomes in spouse caregivers of people with ALS. Thirty-five spouse caregivers rated their own levels of depression and anxiety, subjective burden and marital satisfaction. Caregivers also rated their partner's everyday behaviour. The patients were assessed for disease severity and cognitive function, with composite scores derived for executive function and social cognition. Regression analyses revealed that caregiver burden was predicted by the severity of patients' limb involvement and behavioural problems. Depression was predicted by patients' limb involvement, while behavioural problems and patient age predicted caregiver anxiety. Current marital satisfaction was predicted by patient behavioural problems beyond the level of pre-illness marital satisfaction. In conclusion, the study highlights the potential impact of ALS patients' functional impairment and behavioural change on ALS caregivers' psychosocial functioning. Clinical communication with ALS families should emphasise both physical and psychological challenges presented by the disease

Brane/flux annihilation transitions and nonperturbative moduli stabilization

By extending the calculation of Kahler moduli stabilization to account for an embiggened antibrane, we reevaluate brane/flux annihilation in a warped throat with one stabilized Kahler modulus. We find that depending on the relative size of various fluxes three things can occur: the decay process proceeds unhindered, the anti-D3-branes are forbidden to decay classically, or the entire space decompactifies. Additionally, we show that the Kahler modulus receives a contribution from the collective 3-brane tension. This allows for a significant change in compactified volume during the transition and possibly mitigates some fine tuning otherwise required to achieve large volume.Comment: 25 pages, 6 figures, LaTeX. v2: references adde

Entire solutions of hydrodynamical equations with exponential dissipation

We consider a modification of the three-dimensional Navier--Stokes equations and other hydrodynamical evolution equations with space-periodic initial conditions in which the usual Laplacian of the dissipation operator is replaced by an operator whose Fourier symbol grows exponentially as \ue ^{|k|/\kd} at high wavenumbers $|k|$. Using estimates in suitable classes of analytic functions, we show that the solutions with initially finite energy become immediately entire in the space variables and that the Fourier coefficients decay faster than \ue ^{-C(k/\kd) \ln (|k|/\kd)} for any $C<1/(2\ln 2)$. The same result holds for the one-dimensional Burgers equation with exponential dissipation but can be improved: heuristic arguments and very precise simulations, analyzed by the method of asymptotic extrapolation of van der Hoeven, indicate that the leading-order asymptotics is precisely of the above form with $C= C_\star =1/\ln2$. The same behavior with a universal constant $C_\star$ is conjectured for the Navier--Stokes equations with exponential dissipation in any space dimension. This universality prevents the strong growth of intermittency in the far dissipation range which is obtained for ordinary Navier--Stokes turbulence. Possible applications to improved spectral simulations are briefly discussed.Comment: 29 pages, 3 figures, Comm. Math. Phys., in pres

Distributed Response Time Analysis of GSPN Models with MapReduce

widely used in the performance analysis of computer and communications systems. Response time densities and quantiles are often key outputs of such analysis. These can be extracted from a GSPN’s underlying semi-Markov process using a method based on numerical Laplace transform inversion. This method typically requires the solution of thousands of systems of complex linear equations, each of rank n, where n is the number of states in the model. For large models substantial processing power is needed and the computation must therefore be distributed. This paper describes the implementation of a Response Time Analysis module for the Platform Independent Petri net Editor (PIPE2) which interfaces with Hadoop, an open source implementation of Google’s MapReduce distributed programming environment, to provide distributed calculation of response time densities in GSPN models. The software is validated with analytically calculated results as well as simulated ones for larger models. Excellent scalability is shown. I