Miracle-dz/UniFAR-FTUs huggingface dataset:
Southern Rhine Graben: small-wavelength tomographic study and implications for the dynamic evolution of the graben

SUMMARY Inversion of P-wave traveltime residuals of teleseismic events recorded by a dense network of short-period stations yielded a detailed image of the 3-D velocity structure of the lithosphere-asthenosphere system beneath the southern Rhine Graben area. The upper part of the lithosphere, marked by velocity anomalies orientated along the graben strike, can be related to the development of the graben. These upper 50 km display stronger lateral heterogeneities than the weak anomalies observed at deeper levels which show roughtly an E-W orientation. The teleseismic inversion models yield no indications for significantly reduced seismic velocities in the upper mantle as could be expected from an actively upwelling mantle diapir located beneath the southern Rhine Graben area. The observation of generally weak velocity variations at greater depth indicates a rather smooth transition from the lower lithosphere to the upper asthenosphere. Deeper parts of the lithosphere were probably altered by metasomatic processes as a consequence of the intrusion of melts during middle and late Miocene times. These melts cooled and solidified from the end of the Miocene when rifting and thermal doming ceased in the southern Rhine Graben area.
Magnetoelastic Energy harvesting: Modeling and Experiments

Magnetoelastic materials belong to the wide category of smart materials because of their capability of coupling mechanical quantities (force, strain) to magnetic ones (field, induction) and viceversa. Recently, they have received a lot of interest for actuating and sensing purposes. Moreover, in the general framework of recovering some environmental energy, this kind of smart materials have been considered to recover the mechanical energy of vibrations [51].
Flow regimes, bed morphology, and flow resistance in self‐formed step‐pool channels

We used a mobile bed flume with scaled grain size distribution, channel geometry, and flow to examine morphology and hydraulics of stepped channels. We hypothesized that (1) step geometry and flow resistance differs significantly as a function of the range of grain sizes present, (2) a transition from nappe to skimming flow occurs in stepped channels with mobile beds for conditions similar to stepped spillways, and (3) the partitioning of flow resistance changes significantly when flow passes from nappe to skimming conditions. Results support each of these hypotheses and help to illuminate the complexity of V‐Q relationships in stepped channels, in which a dramatic decrease in flow resistance and increase in velocity accompany the transition from nappe to skimming flow near step‐forming events. Therefore, a single flow resistance equation applicable to both ordinary and large floods may not be ideal in stepped channels. Nonetheless, models based on dimensionless velocity and unit discharge appear more robust compared to those based on the Darcy‐Weisbach friction factor.
Pb isotopes define basement domains of the Altiplano

Detailed Pb isotopic maps of the central Andes, based on 345 (163 previously published, 182 new) analyses of ores, volcanic rocks, and their host rocks, elucidate the gross structure of the basement and reveal that several isotopically distinct basement domains are juxtaposed in this region. The data clearly show that most of the Pb in central Andean igneous and ore samples is derived from the local basement, including Pb in ore deposits of the Bolivian tin belt. Some of the isotopic domain boundaries correspond to geologic structures and the residual gravity pattern, as well as to metallogenic boundaries such as the western edge of the Bolivian tin belt.
Luminescence variations in fast‐growing stalagmites from uppsala, sweden

Abstract Two fast‐growing stalagmites from a cellar vault in Uppsala, southeast Sweden, are analysed for their luminescent properties. The results indicate that variations in luminescence intensity in the stalagmites are annual. Due to problems in finding a suitable absolute dating method this assumption cannot yet be firmly tested; however, results from radiocarbon dating of one of the stalagmites do not contradict the proposal that the laminae are annual. If so, the speleothems have been growing for 10–15 years with a growth rate of 3–8 mm per year, which is a similar rate to other fast‐growing speleothems in Great Britain that have formed from the reaction of lime mortar and carbon dioxide. It is likely that the assumed annual laminae of the luminescence record represent a flush of organic material.
A combined linkage disequilibrium and cosegregation method for fine mapping of QTL and approaches to study the long-term accuracy of genomic selection

Both mapping quantitative trait loci (QTL) and genomic selection (GS) contribute to the genetic improvement of livestock by combining molecular and phenotypic information. This thesis includes a study on a method to combine linkage disequilibrium (LD) and cosegregation (CS) information to fine-map QTL, a multi-locus measure of LD and its relationship with long-term accuracy of genomic estimated breeding value (GEBV), and an approach to simulate validation data by sampling according to mendelian inheritance to predict long-term accuracy of GEBV. A gene-frequency model is proposed to fine-map QTL that combines LD and CS information, where LD information is incorporated into the conditional means and variances given marker information, and CS information is incorporated into covariances of gametic deviations of the model. Algorithms are developed to draw Bayesian inferences on this gene-frequency model (BGF). The performance of the BGF method was compared to a regression method using least squares (LSR) or the identity-by-descent (IBD) method of Meuwissen and Goddard in power to detect and precision to map a QTL. Simulations were conducted under a range of marker densities, sample sizes and sizes of QTL. When there was only LD information in the data, the BGF method had power close or equal to that of LSR, and precision higher than that of LSR. The IBD method is another method that combines LD and CS information. When there was LD and CS information in the data, the BGF method had higher power and precision than the IBD method. A multi-locus measure of LD, R2 w, is proposed to quantify the long-term accuracy of genomic estimated breeding value (GEBV). Scanning through a genome with every SNP chosen to be a surrogate QTL, its genotypes are regressed on all the remaining SNPs, but are predicted using only the surrounding SNPs within a certain length of chromosomal segment. The value of R2 w is obtained by averaging the squared correlation between the true and predicted genotypes over
Improving ocean angular momentum estimates using a model constrained by data

Ocean angular momentum (OAM) calculations using forward model runs without any data constraints have recently revealed the effects of OAM variability on the Earth's rotation. Here we use an ocean model and its adjoint to estimate OAM values by constraining the model to available oceanic data. The optimization procedure yields substantial changes in OAM, related to adjustments in both motion and mass fields, as well as in the wind stress torques acting on the ocean. Constrained and unconstrained OAM values are discussed in the context of closing the planet's angular momentum budget. The estimation procedure yields noticeable improvements in the agreement with the observed Earth rotation parameters, particularly at the seasonal timescale. The comparison with Earth rotation measurements provides an independent consistency check on the estimated ocean state and underlines the importance of ocean state estimation for quantitative studies of the variable large‐scale oceanic mass and circulation fields, including studies of OAM.
Tropical Cyclone Climatology of the South Pacific Ocean and Its Relationship to El Nino-Southern Oscillation

AbstractClimatological features of tropical cyclones in the South Pacific Ocean have been analyzed based on a new archive for the Southern Hemisphere. A vortex tracking and statistics package is used to examine features such as climatological maps of system intensity and the change in intensity with time, average tropical cyclone system movement, and system density. An examination is presented of the spatial variability of these features, as well as changes in relation to phase changes of the El Nino–Southern Oscillation phenomenon. A critical line is defined in this study based on maps of cyclone intensity to describe the statistical geographic boundary for cyclone intensification. During El Nino events, the critical line shifts equatorward, while during La Nina events the critical line is generally displaced poleward. Regional variability in tropical cyclone activity associated with El Nino–Southern Oscillation phases is examined in relation to the variability of large-scale atmospheric or oceanic varia.
effects of long-term bronchodilators in bronchiectasis patients with airflow limitation based on bronchodilator response at baseline

Purpose: The association between positive bronchodilator response (BDR) at baseline and the effect of long-term bronchodilator therapy has not been well elucidated in patients with bronchiectasis. The aims of our study were to explore the association between positive BDR at baseline and lung-function improvement following long-term (3–12 months) bronchodilator therapy in bronchiectasis patients with airflow limitation. Materials and methods: The medical records of 166 patients with clinically stable bronchiectasis who underwent baseline pre- and postbronchodilator spirometry and repeated spirometry after 3–12 months of bronchodilator therapy were retrospectively reviewed. For analysis, patients were divided into two groups, responders and poor responders, based on achievement of at least 12% and 200 mL in forced expiratory volume in 1 second (FEV 1 ) following bronchodilator therapy from baseline FEV 1 . Results: A total of 57 patients (34.3%) were responders. These patients were more likely to have positive BDR at baseline than poor responders (38.6% [22 of 57] vs 18.3% [20 of 109], P = 0.004). This association persisted after adjustment for other confounding factors (adjusted odds ratio 2.298, P = 0.034). However, we found FEV 1 improved significantly following long-term bronchodilator therapy, even in patients without positive BDR at baseline (change in FEV 1 130 mL, interquartile range - 10 to 250 mL; P , 0.001). Conclusion: Positive BDR at baseline was independently associated with responsiveness to long-term bronchodilator therapy in bronchiectasis patients with airflow limitation. However, FEV 1 improvement was also evident in bronchiectasis patients without positive BDR at baseline, suggesting that these patients can benefit from long-term bronchodilator therapy. airway-wall thickening, chronic colonization of Pseudomonas aeruginosa in the bronchial epithelium, excessive airway collapse during expiration, and bronchial hyperreactivity may contribute to deterioration of lung function in patients with bronchiectasis. bronchiectasis and airflow limitation. These findings are consistent with results from studies on COPD patients. The predictive ability of airflow reversibility in a short-acting bronchodilator test
The impact of environmental policy on nitrogen balances at farm level in the European Union

THE IMPACT OF ENVIRONMENTAL POLICY ON NITROGEN BALANCES AT FARM LEVEL IN THE EUROPEAN UNION Hellegers, P.J.G.J. The Hague, Agricultural Economics Research Institute (LEI-DLO), 1996 Onderzoekverslag 153 ISBN 90-5242-377-6 102 p., tab. , f ig. , appendices The impact of environmental policy instruments for the control of nitrate pollut ion f rom agricultural sources on income and nitrogen balances is assessed at farm level in the European Union. A Linear-Programming model at farm level has been used. Individual farm optimizations are based on the 1990/91 sample of the Farm Accountancy Data Network (FADN) of the European Commission. Variable costs are obtained f rom the Sectoral Production and Income model for agriculture (SPEL). A standard on the application of nitrogen f rom organic manure and a levy on the nitrogen surplus are assessed. CAP Reform is considered in the analysis. Three farming types are distinguished; dairy, granivore and cereal farms. The way farms are affected by policy instruments varies largely across groups of farms in the European Union because of the differences in farm structure, input use and the way organic manure is treated at the farm. Adjustment possibilities as a result of policy changes are mainly l imited to f lows of organic manure in the assessments made. The supply of animal manure in EUR 12 exceeds 170 kg of nitrogen per hectare (excluding emission losses) on approximately 19% of the number of dairy holdings and 87% of the number of granivore holdings represented by FADN. This is the equivalent of almost 115 thousand dairy and 53 thousand granivore holdings. The increasing pressure on the manure market in response t o the policy scenarios assessed is mainly the result of the increase in the amount of manure disposed at dairy farms and to a lesser extent at granivore farms. Granivore farms were already affected by existing environmental policy. Several adjustments in farming practice are t o be expected t o meet the requirements of policy. The impact of a more efficient use of feed concentrates, the replacement of inorganic fertilizers by organic manure at arable farms and of emission reducing techniques is presented separately. Nitrogen balance/Agriculture/Environmental Policy/Nitrate Directive/Farm level The contents of this report may be quoted or reproduced wi thout further permission. Due acknowledgement is requested.
Associations between Dopamine D4 Receptor Gene Variation with Both Infidelity and Sexual Promiscuity

Background Human sexual behavior is highly variable both within and between populations. While sex-related characteristics and sexual behavior are central to evolutionary theory (sexual selection), little is known about the genetic bases of individual variation in sexual behavior. The variable number tandem repeats (VNTR) polymorphism in exon III of the human dopamine D4 receptor gene (DRD4) has been correlated with an array of behavioral phenotypes and may be predicatively responsible for variation in motivating some sexual behaviors, particularly promiscuity and infidelity. Methodology/Principal Findings We administered an anonymous survey on personal history of sexual behavior and intimate relationships to 181 young adults. We also collected buccal wash samples and genotyped the DRD4 VNTR. Here we show that individuals with at least one 7-repeat allele (7R+) report a greater categorical rate of promiscuous sexual behavior (i.e., having ever had a “one-night stand”) and report a more than 50% increase in instances of sexual infidelity. Conclusions/Significance DRD4 VNTR genotype varies considerably within and among populations and has been subject to relatively recent, local selective pressures. Individual differences in sexual behavior are likely partially mediated by individual genetic variation in genes coding for motivation and reward in the brain. Conceptualizing these findings in terms of r/K selection theory suggests a mechanism for selective pressure for and against the 7R+ genotype that may explain the considerable global allelic variation for this polymorphism.
Urban Planning And The Development Process

Part 1 The development framework: Introduction - Land and property markets Land and property development processes Urban planning in a market economy. Part 2 Actor perspectives: The land-owner The developer The public sector. Part 3 Local development planning: The practice of local development planning The politics of local development planning The power to influence local development planning The effectiveness of local development planning. Part 4 Looking to the future: An agenda for urban planning practice, education and research.
Derivation of tree stem structural parameters from static terrestrial laser scanning data

Accurate tree-level characteristic information is increasingly demanded for forest management and environment protection. The cutting-edge remote sensing technique of terrestrial laser scanning (TLS) shows the potential of filling this gap. This study focuses on exploring the methods for deriving various tree stem structural parameters, such as stem position, diameter at breast height (DBH), the degree of stem shrinkage, and the elevation angle and azimuth angle of stem inclination. The data for test was collected with a Leica HDS6100 TLS system in Seurasaari, Southern Finland in September 2010. In the field, the reference positions and DBHs of 100 trees were measured manually. The isolation of individual trees is based on interactive segmentation of point clouds. The estimation of stem position and DBH is based on the schematic of layering and then least-square-based circle fitting in each layer. The slope of robust fit line between the height of each layer and DBH is used to characterize the stem shrinkage. The elevation angle of stem inclination is described by the angle between the ground plane and the fitted stem axis. The angle between the north direction and the fitted stem axis gives the azimuth angle of stem inclination. The estimation of the DBHs performed with R square (R2) of 0.93 and root mean square error (RMSE) of 0.038m. The average angle corresponding to stem shrinkage is -1.86°. The elevation angles of stem inclinations are ranged from 31° to 88.3°. The results have basically validated TLS for deriving multiple structural parameters of stem, which help better grasp tree specialties.
Experimental Study of Sound Waves in Sandy Sediment

Abstract : This dissertation describes experiments intended to help understand the physics of sound (compressional waves) propagating through sandy sediments (unconsolidated porous media). The theory (using a lumped parameter model) and measurements (using a reflection ratio technique) includes derivations and measurements of acoustic impedance, effective densities, wave speeds (phase velocities), effective pressures, mode shapes, pressure reflection coefficients, and material moduli. The results show the acoustic impedance divided by the phase velocity, rendering an "effective density," is less than the total density of the sediment (effective density 89% plus or minus 3% of total). The results also show the fluid in the sediment oscillates back-and-forth 2.2 plus or minus 0.4 times farther than the sand in the sediment (mode shape) during the passing of a sound wave. These facts suggest the existence of Biot waves (two compressional waves) in water- saturated sand.
AtomSurf : Surface Representation for Learning on Protein Structures

An essential aspect of learning from protein structures is the choice of their representation as a geometric object (be it a grid, graph, or surface), which conditions the associated learning method. The performance of a given approach will then depend on both the representation and its corresponding learning model. In this paper, we investigate representing proteins as $\textit{surfaces embedded in 3D}$ and evaluate this representation within an established benchmark: atom3d. Our first finding is that despite promising results, state-of-the-art surface-based learning approaches alone are not competitive with other modalities on this benchmark. Building on this, we introduce a novel synergistic approach that incorporates graph and surface-based approaches within a single learnable architecture. We show that using this combination, which inherits the strengths of the two representations, we obtain state-of-the-art results across $\textit{all tested tasks}$, on the atom3d benchmark, as well as on binding pocket classification. Our code and data can be found online: https://github.com/Vincentx15/atom2D.
A systems analysis of NADH dehydrogenase mutants reveals flexibility and limits 1 of Pseudomonas taiwanensis VLB120’s metabolism

Systems Analysis of NADH Dehydrogenase Mutants Reveals Flexibility and Limits of Pseudomonas taiwanensis VLB120's Metabolism. Abstract Obligate aerobic organisms rely on a functional electron transport chain for energy 35 conservation and NADH oxidation. Because of this essential requirement, the genes of 36 this pathway are likely constitutively and highly expressed to avoid a cofactor imbalance 37 and energy shortage under fluctuating environmental conditions. We here investigated 38 the essentiality of the three NADH dehydrogenases of the respiratory chain of the obligate 39 aerobe Pseudomonas taiwanensis VLB120 and the impact of the knockouts of 40 corresponding genes on its physiology and metabolism. While a mutant lacking all three 41 NADH dehydrogenases seemed to be nonviable, the generated single or double 42 knockout strains displayed no, or only a weak, phenotype. Only the mutant deficient in 43 both type-2 dehydrogenases showed a clear phenotype with biphasic growth behavior 44 and a strongly reduced growth rate in the second phase. In-depth analyses of the 45 metabolism of the generated mutants including quantitative physiological experiments, 46 transcript analysis, proteomics, and enzyme activity assays revealed distinct responses 47 to type-2 and type-1 dehydrogenase deletions. An overall high metabolic flexibility 48 enables P. taiwanensis to cope with the introduced genetic perturbations and maintain 49 stable phenotypes, likely by re-routing of metabolic fluxes. This metabolic adaptability has 50 implications for biotechnological applications. While the phenotypic robustness is 51 favorable in large-scale applications with inhomogeneous conditions, the possible 52 versatile redirecting of carbon fluxes upon genetic interventions can thwart metabolic 53 engineering efforts.
DeepPCR: Parallelizing Sequential Operations in Neural Networks

Parallelization techniques have become ubiquitous for accelerating inference and training of deep neural networks. Despite this, several operations are still performed in a sequential manner. For instance, the forward and backward passes are executed layer-by-layer, and the output of diffusion models is produced by applying a sequence of denoising steps. This sequential approach results in a computational cost proportional to the number of steps involved, presenting a potential bottleneck as the number of steps increases. In this work, we introduce DeepPCR, a novel algorithm which parallelizes typically sequential operations in order to speed up inference and training of neural networks. DeepPCR is based on interpreting a sequence of $L$ steps as the solution of a specific system of equations, which we recover using the Parallel Cyclic Reduction algorithm. This reduces the complexity of computing the sequential operations from $\mathcal{O}(L)$ to $\mathcal{O}(\log_2L)$, thus yielding a speedup for large $L$. To verify the theoretical lower complexity of the algorithm, and to identify regimes for speedup, we test the effectiveness of DeepPCR in parallelizing the forward and backward pass in multi-layer perceptrons, and reach speedups of up to $30\times$ for the forward and $200\times$ for the backward pass. We additionally showcase the flexibility of DeepPCR by parallelizing training of ResNets with as many as 1024 layers, and generation in diffusion models, enabling up to $7\times$ faster training and $11\times$ faster generation, respectively, when compared to the sequential approach.