Two decades of numerical modelling to understand long term fluvial archives: Advances and future perspectives

The development and application of numerical models to investigate fluvial sedimentary archives has increased during the last decades resulting in a sustained growth in the number of scientific publications with keywords, 'fluvial models', 'fluvial process models' and 'fluvial numerical models'. In this context we compile and review the current contributions of numerical modelling to the understanding of fluvial archives. In particular, recent advances, current limitations, previous unexpected results and future perspectives are all discussed. Numerical modelling efforts have demonstrated that fluvial systems can display non-linear behaviour with often unexpected dynamics causing significant delay, amplification, attenuation or blurring of externally controlled signals in their simulated record. Numerical simulations have also demonstrated that fluvial records can be generated by intrinsic dynamics without any change in external controls. Many other model applications demonstrate that fluvial archives, specifically of large fluvial systems, can be convincingly simulated as a function of the interplay of (palaeo) landscape properties and extrinsic climate, base level and crustal controls. All discussed models can, after some calibration, produce believable matches with real world systems suggesting that equifinality - where a given end state can be reached through many different pathways starting from different initial conditions and physical assumptions - plays an important role in fluvial records and their modelling. The overall future challenge lies in the development of new methodologies for a more independent validation of system dynamics and research strategies that allow the separation of intrinsic and extrinsic record signals using combined fieldwork and modelling

Geolocators lead to better measures of timing and renesting in black-tailed godwits and reveal the bias of traditional observational methods

Long-term population studies can identify changes in population dynamics over time. However, to realize meaningful conclusions, these studies rely on accurate measurements of individual traits and population characteristics. Here, we evaluate the accuracy of the observational methods used to measure reproductive traits in individually marked black-tailed godwits (Limosa limosa limosa). By comparing estimates from traditional methods with data obtained from light-level geolocators, we provide an accurate estimate of the likelihood of renesting in godwits and the repeatability of the lay dates of first clutches. From 2012 to 2018, we used periods of shading recorded on the light-level geolocators carried by 68 individual godwits to document their nesting behaviour. We then compared these estimates to those simultaneously obtained by our long-term observational study. We found that among recaptured geolocator-carrying godwits, all birds renested after a failed first clutch, regardless of the date of nest loss or the number of days already spent incubating. We also found that 43% of these godwits laid a second replacement clutch after a failed first replacement, and that 21% of these godwits renested after a hatched first clutch. However, the observational study correctly identified only 3% of the replacement clutches produced by geolocator-carrying individuals and designated as first clutches a number of nests that were actually replacement clutches. Additionally, on the basis of the observational study, the repeatability of lay date was 0.24 (95% CI 0.17-0.31), whereas it was 0.54 (95% CI 0.28-0.75) using geolocator-carrying individuals. We use examples from our own and other godwit studies to illustrate how the biases in our observational study discovered here may have affected the outcome of demographic estimates, individual-level comparisons, and the design, implementation and evaluation of conservation practices. These examples emphasize the importance of improving and validating field methodologies and show how the addition of new tools can be transformational

The makewaves tsunami tests and their relevance to tsunami engineering and risk management

MAKEWAVES is an international multi-partner collaborative project bringing together nine academic institutions and two commercial consultancies. The objective of the collaboration is to develop experimental data and associated numerical modelling on tsunami inundation and interaction with boulders, buildings, natural and engineered barriers, towards the development of new internationally accepted guidance for structural codes and standards. Using a pneumatic tsunami simulator (TS) developed jointly by HR Wallingford and UCL the team conducted experiments between November 2022 and April 2023 within a highly instrumented 100m long flume. The TS is capable of simulating realistic trough and crest-led tsunami waves at 1:50, including traces from the The TS is capable of generating very long trough and crest-led waves, and can reproduce at 1:50 scale waves from real life events such as the Mercator trace from the 2004 Indian Ocean event and the and 2011 Tohoku tsunamis. The TS capability has been further extended to include bore-waves. The characteristics of the waves are controlled by adjusting the flow rate and total volume of water drawn in and discharged by the TS. The experimental campaign is was subdivided into discrete research areas, each aimed at furthering knowledge on how different tsunami wave characteristics affect their interaction with manmade and natural structures environments. These include tests aimed at understanding: (1) how roughness representative of coastal forests and mangroves affects tsunami inundation characteristics, (2) how tsunami interact with boulders (3) the effectiveness of offshore breakwaters as tsunami barriers (4) how structural loads and foundation scour are affected by building permeability. This paper presents an overview of the tests conducted and some of the important early observations made that are relevant to future engineering standards and to tsunami disaster management

Long-term evidence for ecological intensification as a pathway to sustainable agriculture

Ecological intensification (EI) could help return agriculture into a ‘safe operating space’ for humanity. Using a novel application of meta-analysis to data from 30 long-term experiments from Europe and Africa (comprising 25,565 yield records), we investigated how field-scale EI practices interact with each other, and with N fertilizer and tillage, in their effects on long-term crop yields. Here we confirmed that EI practices (specifically, increasing crop diversity and adding fertility crops and organic matter) have generally positive effects on the yield of staple crops. However, we show that EI practices have a largely substitutive interaction with N fertilizer, so that EI practices substantially increase yield at low N fertilizer doses but have minimal or no effect on yield at high N fertilizer doses. EI practices had comparable effects across different tillage intensities, and reducing tillage did not strongly affect yields

Between local zones and MN units: A new inter-basinal rodent zonation for the late Neogene of Spain

Since the appearance of the first major magnetostratigraphic studies covering the late Neogene of Spain (e.g., Opdyke et al., 1997; Garcés et al., 1998) the number of Spanish continental sections with a correlation to the Geomagnetic Time Scale has steadily grown. Nonetheless, well-calibrated sections with a dense record are still rare, between-basin biostratigraphic correlation is not straightforward, and ages of uncalibrated sites are poorly constrained. Given the overall similarity of rodent assemblages between Iberian basins during the interval MN11–MN17 (9–2 Ma), the definition of a system of Iberian rodent zones for this interval is a logical and necessary step leading to improved correlations. Our revision thus entails the integration of local biozonations into a single Iberian biostratigraphic framework. The inferred series of zone boundary ages are used to improve the age estimates for most Iberian micromammal sites. The chronological backbone in our approach is formed by the available Iberian magnetochronologic records (Teruel, Cabriel, Júcar, Jumilla-La Celia, Fortuna and Guadix-Baza Basins). After analyzing similarities in taxonomic composition and turnover across basins with a defined biozonation (Teruel, Bajo Segura, Alcoy, Granada and Guadix-Baza Basins), 15 Iberian biozones were defined for the 9–2 Ma interval. Age uncertainty intervals for each boundary and for most Iberian micromammal sites were inferred using additional information on local sedimentation and/or evolutionary rates. Among our results are new ages for the latest Tortonian and earliest Messinian (MN12–MN13 transition, 8–7 Ma), a thus far poorly dated interval on the Iberian Peninsula. The new chronology for this interval is based on the integrated stratigraphic records of the Jumilla-La Celia and Teruel Basins. Sections in the Jumilla-La Celia basin (eastern Betic Cordillera; Van Balen et al., 2015) were sampled paleomagnetically, further constraining the ages of various MN12-correlative sites (Van Dam et al., 2014). Finally, regular bedding patterns in sections near Concud in the Teruel Basin (eastern Central Spain) were interpreted cyclostratigraphically and used as a tool in addition to magnetostratigraphy for dating several classical and newly sampled MN12-correlative mammal sites in the area

A transcriptomic based deconvolution framework for assessing differentiation stages and drug responses of AML

The diagnostic spectrum for AML patients is increasingly based on genetic abnormalities due to their prognostic and predictive value. However, information on the AML blast phenotype regarding their maturational arrest has started to regain importance due to its predictive power for drug responses. Here, we deconvolute 1350 bulk RNA-seq samples from five independent AML cohorts on a single-cell healthy BM reference and demonstrate that the morphological differentiation stages (FAB) could be faithfully reconstituted using estimated cell compositions (ECCs). Moreover, we show that the ECCs reliably predict ex-vivo drug resistances as demonstrated for Venetoclax, a BCL-2 inhibitor, resistance specifically in AML with CD14+ monocyte phenotype. We validate these predictions using LUMC proteomics data by showing that BCL-2 protein abundance is split into two distinct clusters for NPM1-mutated AML at the extremes of CD14+ monocyte percentages, which could be crucial for the Venetoclax dosing patients. Our results suggest that Venetoclax resistance predictions can also be extended to AML without recurrent genetic abnormalities and possibly to MDS-related and secondary AML. Lastly, we show that CD14+ monocytic dominated Ven/Aza treated patients have significantly lower overall survival. Collectively, we propose a framework for allowing a joint mutation and maturation stage modeling that could be used as a blueprint for testing sensitivity for new agents across the various subtypes of AML.This study was funded by a strategic investment of the Leiden University Medical Center, embedded within the Leiden Oncology Center, and executed within the Leiden Center for Computational Oncology. EvdA was funded by a personal grant of the Dutch Research Council (NWO; VENI: 09150161810095).Peer reviewe

Speeding Up Microevolution: The Effects of Increasing Temperature on Selection and Genetic Variance in a Wild Bird Population

The authors show that environmental variation may lead to a positive association between the annual strength of selection and expression of genetic variance in a wild bird population, which can speed up microevolution and have important consequences for how fast natural populations adapt to environmental changes

The risk factor profile of women with secondary infertility: an unmatched case-control study in Kigali, Rwanda

<p>Abstract</p> <p>Background</p> <p>Secondary infertility is a common, preventable but neglected reproductive health problem in resource-poor countries. This study examines the association of past sexually transmitted infections (STIs) including HIV, bacterial vaginosis (BV) and factors in the obstetric history with secondary infertility and their relative contributions to secondary infertility.</p> <p>Methods</p> <p>Between November 2007 and May 2009 a research infertility clinic was set up at the Kigali University Teaching Hospital in Rwanda. Cases were defined as sexually-active women aged 21-45 years presenting with secondary infertility (n = 177), and controls as multiparous women in the same age groups who recently delivered (n = 219). Participants were interviewed about socio-demographic characteristics and obstetric history using structured questionnaires, and were tested for HIV and reproductive tract infections (RTIs).</p> <p>Results</p> <p>Risk factors in the obstetric history for secondary infertility were lack of prenatal care in the last pregnancy, the first pregnancy before the age of 21 years, a history of unwanted pregnancy, a pregnancy with other than current partner, an adverse pregnancy outcome, stillbirth, postpartum infection and curettage. Presence of HIV, herpes simplex virus type 2 (HSV-2), or <it>Treponema pallidum </it>antibodies, and bacterial vaginosis (BV), were significantly more common in women in secondary infertile relationships than those in fertile relationships. The population attributable fractions (PAF%) for obstetric events, HIV, other (STIs), and BV were 25%, 30%, 27%, and 14% respectively.</p> <p>Conclusions</p> <p>The main finding of this study is that obstetric events, HIV and other STIs contribute approximately equally to secondary infertility in Rwanda. Scaling up of HIV/STI prevention, increased access to family planning services, improvement of prenatal and obstetric care and reduction of stillbirth and infant mortality rates are all likely to decrease secondary infertility in sub-Saharan Africa.</p