Investigating the evolution of major Northern Hemisphere ice sheets during the last glacial-interglacial cycle

A 2.5-dimensional climate model of intermediate complexity, CLIMBER-2, fully coupled with the GREMLINS 3-D thermo-mechanical ice sheet model is used to simulate the evolution of major Northern Hemisphere ice sheets during the last glacial-interglacial cycle and to investigate the ice sheets responses to both insolation and atmospheric CO<sub>2</sub> concentration. This model reproduces the main phases of advance and retreat of Northern Hemisphere ice sheets during the last glacial cycle, although the amplitude of these variations is less pronounced than those based on sea level reconstructions. At the last glacial maximum, the simulated ice volume is 52.5×10<sup>15</sup> m<sup>3</sup> and the spatial distribution of both the American and Eurasian ice complexes is in reasonable agreement with observations, with the exception of the marine parts of these former ice sheets. <br> A set of sensitivity studies has also been performed to assess the sensitivity of the Northern Hemisphere ice sheets to both insolation and atmospheric CO<sub>2</sub>. Our results suggest that the decrease of summer insolation is the main factor responsible for the early build up of the North American ice sheet around 120 kyr BP, in agreement with benthic foraminifera δ<sup>18</sup>O signals. In contrast, low insolation and low atmospheric CO<sub>2</sub> concentration are both necessary to trigger a long-lasting glaciation over Eurasia

Inclusive 2H(3He,t) reaction at 2 GeV

The inclusive 2H(3He,t) reaction has been studied at 2 GeV for energy transfers up to 500 MeV and scattering angles from 0.25 up to 4 degrees. Data are well reproduced by a model based on a coupled-channel approach for describing the NN and N Delta systems. The effect of final state interaction is important in the low energy part of the spectra. In the delta region, the cross-section is very sensitive to the effects of Delta-N interaction and Delta N - NN process. The latter has also a large influence well below the pion threshold. The calculation underestimates the experimental cross-section between the quasi-elastic and the delta peaks; this is possibly due to projectile excitation or purely mesonic exchange currents.Comment: 9 pages, 9 figures, accepted for publication in EPJ

Evolutionarily informed deep learning methods for predicting relative transcript abundance from DNA sequence

Deep learning methodologies have revolutionized prediction in many fields and show potential to do the same in molecular biology and genetics. However, applying these methods in their current forms ignores evolutionary dependencies within biological systems and can result in false positives and spurious conclusions. We developed two approaches that account for evolutionary relatedness in machine learning models: (i) gene-family–guided splitting and (ii) ortholog contrasts. The first approach accounts for evolution by constraining model training and testing sets to include different gene families. The second approach uses evolutionarily informed comparisons between orthologous genes to both control for and leverage evolutionary divergence during the training process. The two approaches were explored and validated within the context of mRNA expression level prediction and have the area under the ROC curve (auROC) values ranging from 0.75 to 0.94. Model weight inspections showed biologically interpretable patterns, resulting in the hypothesis that the 3′ UTR is more important for fine-tuning mRNA abundance levels while the 5′ UTR is more important for large-scale changes

The application of different 3D-scan-systems and photogrammetry at an excavation — A Neolithic dolmen from Switzerland

The discovery of a Neolithic dolmen in Switzerland with inhumations, dating between 3500 and 3000 BCE, was an exceptional finding. To provide best conditions for subsequent studies on the archaeological remains our interdisciplinary team decided to apply 3D documentation. Depending on different factors, two scanning systems with four scanners and photogrammetry were applied and the obtained data was combined. Detailed excavation plans and simultaneously a reduction of excavation time without loss of information were the result. A virtual animation of the dolmen in its reconstructed ancient appearance combined with the context of the grave goods was created. The 3D documentation provided initial data for anthropological and paleogenetic analyses. The individuals buried in the dolmen might provide novel information to the Neolithic research of central Europe. Additionally, with the help of the 3D data, the dolmen was rebuilt to make this archaeological heritage accessible to the public

The well-preserved Late Neolithic dolmen burial of Oberbipp, Switzerland. Construction, use, and post-depositional processes

Excavation of the Late Neolithic dolmen of Oberbipp BE, Steingasse in the Swiss Central Plateau provided a unique opportunity for a comprehensive study of the archaeological and anthropological evidence. In multidisciplinary studies, we investigated the processes at work during construction, use, and abandonment of the megalithic structure, as well as the dietary habits, subsistence strategy, and possible mobility of the Neolithic population. Archaeological methods included micromorphology, archaeobiology, typology, use-wear analysis, and geology. The anthropological investigation was complemented by an analysis of stable isotope ratios and palaeogenetics. Local topography and the cover of alluvial sediments ensured an extraordinary conservation of the monument. It allowed the preservation of the human remains of at least 42 individuals of both sexes and all ages. The observation of the sedimentary and post-depositional processes, supplemented by an extensive series of radiocarbon dates, allowed us to reconstruct the history of the dolmen in its environment and the definition of at least two deposition phases. We found genetic evidence of lactase intolerance, a local population with a mixed ancestry of early Anatolian farmers and Western hunter-gatherers, and a crop-based diet. Sparse remains of a nearby Late Neolithic settlement sustain the interpretation that this is the burial site of a local farming community. Evidence of higher mobility of females and kinship over three generations solely in the paternal line suggests a virilocal community. Bone-altering pathologies support the assumption of a caring society

The HADES Tracking System

The tracking system of the dielectron spectrometer HADES at GSI Darmstadt is formed out of 24 low-mass, trapezoidal multi-layer drift chambers providing in total about 30 square meter of active area. Low multiple scattering in the in total four planes of drift chambers before and after the magnetic field is ensured by using helium-based gas mixtures and aluminum cathode and field wires. First in-beam performance results are contrasted with expectations from simulations. Emphasis is placed on the energy loss information, exploring its relevance regarding track recognition.Comment: 6 pages, 4 figures, presented at the 10th Vienna Conference on Instrumentation, Vienna, February 2004, to be published in NIM A (special issue

A versatile method for simulating pp -> ppe+e- and dp -> pne+e-p_spec reactions

We have developed a versatile software package for the simulation of di-electron production in $pp$ and $dp$ collisions at SIS energies. Particular attention has been paid to incorporate different descriptions of the Dalitz decay $\Delta \to N e^+e^-$ via a common interface. In addition, suitable parameterizations for the virtual bremsstrahlung process $NN \to NN e^+e^-$ based on one-boson exchange models have been implemented. Such simulation tools with high flexibility of the framework are important for the interpretation of the di-electron data taken with the HADES spectrometer and the design of forthcoming experiments

The Λp\bf{\Lambda p} interaction studied via femtoscopy in p + Nb reactions at sNN=3.18 GeV\mathbf{\sqrt{s_{NN}}=3.18} ~\mathrm{\bf{GeV}}

We report on the first measurement of $p\Lambda$ and $pp$ correlations via the femtoscopy method in p+Nb reactions at $\mathrm{\sqrt{s_{NN}}=3.18} ~\mathrm{GeV}$, studied with the High Acceptance Di-Electron Spectrometer (HADES). By comparing the experimental correlation function to model calculations, a source size for $pp$ pairs of $r_{0,pp}=2.02 \pm 0.01(\mathrm{stat})^{+0.11}_{-0.12} (\mathrm{sys}) ~\mathrm{fm}$ and a slightly smaller value for $p\Lambda$ of $r_{0,\Lambda p}=1.62 \pm 0.02(\mathrm{stat})^{+0.19}_{-0.08}(\mathrm{sys}) ~\mathrm{fm}$ is extracted. Using the geometrical extent of the particle emitting region, determined experimentally with $pp$ correlations as reference together with a source function from a transport model, it is possible to study different sets of scattering parameters. The $p\Lambda$ correlation is proven sensitive to predicted scattering length values from chiral effective field theory. We demonstrate that the femtoscopy technique can be used as valid alternative to the analysis of scattering data to study the hyperon-nucleon interaction.Comment: 12 pages, 11 figure

An upper limit on hypertriton production in collisions of Ar(1.76 AGeV)+KCl

A high-statistic data sample of Ar(1.76 AGeV)+KCl events recorded with HADES is used to search for a hypertriton signal. An upper production limit per centrality-triggered event of $1.04$ x $10^{-3}$ on the $3\sigma$ level is derived. Comparing this value with the number of successfully reconstructed $\Lambda$ hyperons allows to determine an upper limit on the ratio $N_{_{\Lambda}^3H}/N_{\Lambda}$, which is confronted with statistical and coalescence-type model calculations

A sorghum practical haplotype graph facilitates genome‐wide imputation and cost‐effective genomic prediction

Successful management and utilization of increasingly large genomic datasets is essential for breeding programs to accelerate cultivar development. To help with this, we developed a Sorghum bicolor Practical Haplotype Graph (PHG) pangenome database that stores haplotypes and variant information. We developed two PHGs in sorghum that were used to identify genome-wide variants for 24 founders of the Chibas sorghum breeding program from 0.01x sequence coverage. The PHG called single nucleotide polymorphisms (SNPs) with 5.9% error at 0.01x coverage—only 3% higher than PHG error when calling SNPs from 8x coverage sequence. Additionally, 207 progenies from the Chibas genomic selection (GS) training population were sequenced and processed through the PHG. Missing genotypes were imputed from PHG parental haplotypes and used for genomic prediction. Mean prediction accuracies with PHG SNP calls range from .57–.73 and are similar to prediction accuracies obtained with genotyping-by-sequencing or targeted amplicon sequencing (rhAmpSeq) markers. This study demonstrates the use of a sorghum PHG to impute SNPs from low-coverage sequence data and shows that the PHG can unify genotype calls across multiple sequencing platforms. By reducing input sequence requirements, the PHG can decrease the cost of genotyping, make GS more feasible, and facilitate larger breeding populations. Our results demonstrate that the PHG is a useful research and breeding tool that maintains variant information from a diverse group of taxa, stores sequence data in a condensed but readily accessible format, unifies genotypes across genotyping platforms, and provides a cost-effective option for genomic selection