Miracle-dz/UniFAR-FTUs huggingface dataset:
Computational Physics: Stochastic Simulation

The real purpose of modelling and simulation is to discover that nature hasn't misled you into thinking you know something, you don't actually know. In the ever growing field of computer simulation stochastic simulation plays a more and more prominent role. This is mainly due to the enormous potential of nowadays computer systems. The type of systems that need to be studied through stochastic simulation are systems of which the behaviour can only be predicted by explicit simulation, rather than analytical calculation. We classify these systems by "computationally irreducible complex systems". Examples are: The motion of molecules in a classical liquid, light beams in ray-tracing optics, spreading phenomena (of diseases, forest fires etc.), growth phenomena (of crystals or macroscopic biological entities), or more general, all problems from physics that can be described in terms of N-body interactions. This text is meant to be background undergraduate material for self study in the field of stochastic simulation of problems in physics. The text is accompanied by addenda with exercises and training material: there is no way you can understand computer simulation without actually doing it! The course can be considered as a good preparation for courses on more advanced topics of simulation such as Computational Physics II: "Understanding Molecular Simulations", "Parallel Scientific Computing and Simulation" and "Simulation of Complex Systems". This text started with the preparation of a lecture on modelling and simulation at the 1994 CERN summer school in Hungary. Large parts of the original idea's and text are adapted from, and motivated by, the literature listed at the end of this document. This text is clearly a compromise where I have chosen stimulating examples from computational physics rather than rigorous treatment of selected topics. Since I plan to update the text each year I would appreciate to receive your comments, suggestions, additions, and corrections. Computer simulation is fun, but we have to stay critical and keep a close watch on the figures and data we produce and ask ourselves if it is physics we are looking at or rather a poor mimic of it. In the words of E. Wigner (after seeing a complicated computer simulation): "I think the computer understands it, now I want to understand it! "
SAR imagery to estimate roughness parameters when modelling runoff risk

The influence of the roughness of agricultural soil on runoff and erosion is a proven fact. Synthetic aperture radar (SAR) sensors should enable discrimination between plots with different cropping patterns. A study of Mediterranean vineyards in southern France was made, with the aim of obtaining a better understanding of the potential for using radar satellite data from ERS-1 when estimating roughness parameters. Roughness measurements enabled modelling of the backscattering coefficient (sigma0) of known surfaces, using the electromagnetic Integral Equation Model (IEM). The good correlation between ERS-1 and IEM data indicated the feasibility of extracting roughness parameters by means of remote sensing methods. Seven ERS-1 images were examined, corresponding to different stages in the development of vegetation and roughness. Two images were finally selected as they offered the possibility of discriminating between two factors: (1) the orientation of mechanical labour, which can be related toa periodic a.
Coastal karst springs in the Mediterranean basin : study of the mechanisms of saline pollution at the Almyros spring (Crete), observations and modelling

Variations in salinity and flow rate in the aerial, naturally salty spring of Almyros of Heraklion on Crete were monitored during two hydrological cycles. We describe the functioning of the coastal karstic system of the Almyros and show the influence of the duality of the flow in the karst (conduits and fractured matrix) on the quality of the water resource in the coastal area. A mechanism of saltwater intrusion into this highly heterogeneous system is proposed and validated with a hydraulic mathematical model, which describes the observations remarkably well.
Environmental exposure to cadmium, forearm bone density, and risk of fractures: prospective population study. Public Health and Environmental Exposure to Cadmium (PheeCad) Study Group.

BACKGROUND Chronic low-level exposure to cadmium may promote calcium loss via urinary excretion. We undertook a prospective population study to investigate whether environmental exposure to cadmium lowers bone density and increases risk of fractures. METHODS We measured urinary cadmium excretion, a biomarker of lifetime exposure, in people from ten districts of Belgium, of which six districts bordered on three zinc smelters. We also measured cadmium in soil and in vegetables from the districts, and collected data on incidence of fractures and height loss. Bone density was measured at the forearm just above the wrist by single photon absorptiometry, and calculated as the mean of six proximal and four distal scans. FINDINGS Mean cadmium excretion at baseline was 8.7 nmol daily. Across the ten districts, mean cadmium concentration in soil ranged from 0.8 to 14.7 mg/kg, and from 0.1 to 4.0 mg/kg dry weight in vegetables. Median follow-up was 6.6 years. Mean forearm bone density in proximal and distal scans was 0.54 g/cm2 and 0.43 g/cm2 in men, and 0.44 g/cm2 and 0.34 g/cm2 in women. In postmenopausal women, a twofold increase in urinary cadmium correlated with 0.01 g/cm2 decrease in bone density (p<0.02). The relative risks associated with doubled urinary cadmium were 1.73 (95% CI 1.16-2.57; p=0.007) for fractures in women and 1.60 (0.94-2.72, p=0.08) for height loss in men. Cadmium excretion in districts near smelters was 22.8% higher (p=0.001) than in other districts, with fracture rates of 16.0 and 10.3 cases per 1000 person-years, respectively, and a population-attributable risk of 35.0%. INTERPRETATION Even at a low degree of environmental exposure, cadmium may promote skeletal demineralisation, which may lead to increased bone fragility and raised risk of fractures.
Late Holocene climate change in the North Atlantic and equatorial Africa: Millennial‐scale ITCZ migration

Climate proxy data and numerical models suggest that latitudinal displacements of the Intertropical Convergence Zone (ITCZ) occur during millennial‐scale cold events in the North Atlantic region, but the potential effects of these ITCZ movements on the climate of equatorial regions are unclear. Here we present a 5400‐year geochemical record of rainfall and drought from Lake Edward in equatorial Africa. We observe a non‐linear correlation in which drought in equatorial Africa occurs during both cold and warm extremes in the North Atlantic's 1500‐year quasi‐cycle. We propose that this relationship occurs due to northward/southward displacement of the ITCZ from its equatorial mean position during warm/cold events. Our results show that millennial‐scale high‐latitude climate events are linked to changes in equatorial terrestrial climate even during the late Holocene and suggest important constraints on the mechanisms linking tropical and extratropical climate variability.
Identification of clear felled areas using SPOT P and Almaz-1 SAR data

Almaz-1 S-band (3.125GHz) satellite SAR data from two subsequent years in combination with optical data have been analysed to determine the separability between recently clear felled areas and forested areas. The test area is situated in northern Sweden within the boreal conifer belt and consists of 32ha of recently clear felled areas and 464ha of forested areas. The basic assumption in this study is that, in an operational case, optical data before the clear felling, and radar data from both before and after the felling, will be available. The optical image is used for segmentation of the forest landscape into homogenous segments. For each segment statistical features based on the first and second order histogram are computed in the two radar images. The changed areas are identified by linear discriminant analysis with cross-validation. Classification based on segment mean values from the Almaz-1 images performed better than using a simple square neighbourhood mean. When using the segment mean values 61.
Transition Phenomena in a Straight Channel with a 40 to 1 Aspect Ratio with and without Imposed Pulsations. Part 1: Near-Wall and Central Region Profiles

Abstract : A channel with a rectangular cross-section, 40 to 1 aspect ration (height is 0.0127 m), and 4.27 m test section (336 channel heights) is used to study the effects of imposed pulsations on transitional flow phenomena. Periodic velocity variations are produced in the test section using a single rotating vane located in the flow downstream of the test section. Flows with Reynolds numbers (Re) ranging from 1100 to 3600 are studied at Stokes numbers of 4.08 and 5.79 and Strouhal numbers from 0.02 to 0.122 by imposing pulsations at 1 Hz and at 2 Hz. Time-averaged velocity profiles both within and outside of the Stokes layer are unaffected by the imposed pulsations at frequencies of 1 and 2 Hz for the entire range of Reynolds numbers studied. Longitudinal turbulence intensity profiles show a local maxima only at the channel centerline for Reynolds numbers from 1250 to 1550. This is evidence of a center mode of instability. Longitudinal turbulence intensity profiles show a local maxima at both the channel centerline and y/d of 0.85 to Reynolds number from 1710 to 2300. As the Reynolds number increases from 2350 to 3400 local maxima of longitudinal turbulence intensity occur only at y/d of 0.9. Normalized profiles of longitudinal turbulence intensity are the same with and without pulsations for all Reynolds number studies with the exception of Reynolds numbers 2400 and 2450. Longitudinal turbulence intensity profiles at a Reynolds number of 2400 show that magnitudes near the channel centerline are reduced at Stokes number of 5.79 (2 Hz pulsations) as compared to without pulsations. At Reynolds number of 2450 the magnitude of longitudinal turbulence intensity near the channel centerline are reduced at Stokes number of 4.08 and 5.79 (1 Hz and 2 Hz pulsations).
Mantle temperature anomalies along the past and paleoaxes of the Galápagos spreading center as inferred from gravity analyses

To better understand the effects of hot spots on mid-ocean ridge thermal structure, we investigate the subsurface density structure of the Galapagos spreading center and nearby lithosphere. Using shipboard gravity and bathymetry data, we obtain maps of mantle Bouguer anomalies (MBA) by removing from the free-air gravity the attractions of seafloor topography and a 6-km-thick model crust. Comparison of observed and theoretical MBA profiles along isochrons for ages 0.0–7.7 Ma suggests that seafloor topography is isostatically compensated by mass anomalies primarily in the upper 100 km of the mantle. This result is consistent with the notion that seafloor topography along the Galapagos spreading center is supported by lateral changes of crustal thickness and upper mantle density, both of which are controlled by temperatures in the upper mantle where decompression melting occurs. Along the ridge axis, the MBA decreases from the east and west toward the Galapagos hot spot by ∼90 mGal, reaching a minimum nearest the hot spot at 91°W. Seafloor topography mirrors the MBA along axis, increasing by ∼1.1 km toward the hot spot. These variations in MBA and bathymetry can be explained by crustal thickening and mantle density variations resulting from a gradual axial temperature increase of 50±25°C toward the hot spot. The predicted crustal thickening of 2–4 km nearest the hot spot accounts for 70–75% of the along-axis MBA and bathymetry anomalies; mantle density variations account for the rest of the anomalies. From the crustal isochron of age 7.7 Ma to the present-day axis, the along-isochron amplitudes of MBA decrease from ∼150 to ∼90 mGal. The corresponding along-isochron bathymetry anomalies decrease from ∼1.7 to ∼1.1 km. These observations along the paleoaxes of the Galapagos spreading center indicate that the axial temperature anomaly was 70% hotter in the past (86±25°C) and has steadily decreased to 50±25°C as the ridge axis migrated away from the Galapagos hot spot. These along-isochron temperature anomalies, however, have remained well below that estimated for the hot spot itself (200°C), indicating that the lateral temperature gradient between the hot spot and the ridge axis has remained 10–20 times greater than that along the ridge axis over the past 7.7 m.y.
A mesoscale eddy dipole in the offshore California Current

There is a transition zone in the California Current system between inshore coastal and offshore oceanic flow. This transition zone is associated with the main core of the California Current and is populated with offshore mesoscale eddies. The structure of isolated eddies and dipole eddy pairs found within the transition zone is examined using water mass analysis (spiciness and dissolved oxygen). The analyses show that these offshore mesoscale eddies have cores which contain California Undercurrent water. These observations and independent observations of the Sitka eddy near Sitka, Alaska, support the conclusion that a bathymetrically induced instability of the California Undercurrent is a likely generation mechanism for the offshore eddies. This conclusion also is consistent with mathematical models of eddy generation in a subsurface, poleward baroclinic current. The similarity between long-term mean conditions (CaICOFI), conditions observed during January 1981 and July 1985, and those of the Sitka eddy, coupled with the bathymetric effects, provides a plausible explanation for the recurrence of offshore mesoscale eddies at preferred locations within the transition zone.
Formation of the 1300-km-wide intracontinental orogen and postorogenic magmatic province in Mesozoic South China: A flat-slab subduction model

We propose a flat-slab subduction model for Mesozoic South China based on both new sensitive high-resolution ion microprobe (SHRIMP) U-Pb zircon data and a synthesis of existing structural, geochronological, and sedimentary facies results. This model not only explains the development of a broad (∼1300-km-wide) intracontinental orogen that migrated from the coastal region into the continental interior between ca. 250 Ma and 190 Ma, but can also account for the puzzling chain of events that followed: the formation of a shallow-marine basin in the wake of the migrating foreland fold-and-thrust belt, and the development of one of the world's largest Basin and Range–style magmatic provinces after the orogeny. The South China record may serve as an example of the multiple effects of flat-slab subduction, including migrating orogenesis and foreland flexure, synorogenic sagging behind the active orogen, postdelamination lithospheric rebound, and the development of a Basin and Range–style broad magmatic province.
Two decades of functional-structural plant modelling: now addressing fundamental questions in systems biology and predictive ecology.

BACKGROUND Functional-structural plant models (FSPMs) explore and integrate relationships between a plant's structure and processes that underlie its growth and development. In the last twenty years, scientists interested in functional-structural plant modelling have expanded greatly the range of topics covered and now handle dynamical models of growth and development occurring from the microscopic scale, and involving cell division in plant meristems, to the macroscopic scales of whole plants and plant communities. SCOPE The FSPM approach occupies a central position in plant science; it is at the crossroads of fundamental questions in system biology and predictive ecology. This special issue of Annals of Botany features selected papers on critical areas covered by FSPMs and examples of comprehensive models that are used to solve theoretical and applied questions, ranging from developmental biology to plant phenotyping and management of plants for agronomic purposes. Altogether, they offer an opportunity to assess the progress, gaps and bottlenecks along the research path originally foreseen for FSPMs two decades ago. This review also allows discussion of current challenges of FSP models regarding i) integration of multi-disciplinary knowledge, ii) methods for handling complex models, iii) standards to achieve interoperability and greater genericity and iv) understanding of plant functioning across scales. CONCLUSIONS This approach has demonstrated considerable progress, but has yet to reach its full potential in terms of integration and heuristic knowledge production. The research agenda of FSP modelers in the coming years should place a greater emphasis on explaining robust emergent patterns, and on the causes of possible deviation from it. Modelling such patterns could indeed fuel both generic integration across scales and transdisciplinary transfer. In particular, it could be beneficil to emergent fields of research such as model-assisted phenotyping and predictive ecology in managed ecosystems.
Enzyme blockade: a nonradioactive method to determine the absolute rate of cholesterol synthesis in the brain

The standard in vivo method to determine rates of brain cholesterol synthesis involves systemic injection of 3 H 2 O and measurement of incorporated radioactivity in sterols. Herein, we describe an alternative method (“en-zyme blockade”) that obviates the use of radioactivity. The method relies on the ability of AY9944, a potent and relatively selective inhibitor of cholesterol synthesis, to cause the time-dependent accumulation of 7-dehydrocholesterol (DHC), a cholesterol precursor detected with sensitivity and speciﬁcity by reverse-phase HPLC-coupled spectrophotom-etry at 282 nm. To validate the method, adult AY9944-treated and control mice were injected with [ 3 H]acetate. After 24 h, most of the radioactivity in brain sterols from treated mice accumulated in DHC, without signiﬁcantly per-turbing overall sterol pathway activity, compared with con-trols (where cholesterol was the dominant radiolabeled sterol, with no label found in DHC). When adult mice were treated continuously with AY9944, the time-dependent accumulation of DHC in brain was linear (after (cid:2) 8 h) for 3 days. The rate of brain cholesterol synthesis determined by this method ( (cid:2) 30 (cid:2) g/g/day) closely agrees with that determined by the radioactive method. We also determined the
Lobular and ductal carcinomas of the breast have distinct genomic and expression profiles

1 Lobular and ductal carcinomas of the breast have distinct genomic and expression profiles François Bertucci, Béatrice Orsetti, Vincent Nègre, Pascal Finetti, Carole Rougé, Jean-Charles Ahomadegbe, Frédéric Bibeau, Marie-Christine Mathieu, Isabelle Treilleux, Jocelyne Jacquemier, Lisa Ursule, Agnès Martinec, Qing Wang, Jean Bénard, Alain Puisieux, Daniel Birnbaum, Charles Theillet. 1 INSERM UMR599; Centre de Recherche en Cancérologie de Marseille, Institut Paoli-Calmettes. Marseille, France. 2 INSERM U896, Institut de Recherche en Cancérologie de Montpellier, CRLC Val d’Aurelle-Paul Lamarque, Montpellier, France 3 Université Paris XI, UPRES 3535, Institut Gustave Roussy, Villejuif, France 4 CRLC Val d’Aurelle-Paul Larmarque, Laboratoire d’Anatomopathologie, Montpellier, France 5 Institut Gustave Roussy, Département de Biopathologie, Villejuif, France 6 Centre Léon Bérard, laboratoire d’Anatomopathologie, Lyon, France 7 Ipsogen S.A. , Marseille-Luminy, France. 8 Centre Léon Bérard, laboratoire d’Oncologie Moléculaire, Lyon, France 9 CNRS UMR 8126, Institut Gustave Roussy, Villejuif, France 10 INSERM U590, Centre Léon Bérard, Lyon, France
Application of a 3D laser scanner in the assessment of erosion and deposition volumes and channel change in a proglacial river

Previous studies of channel morphological change have often relied upon sparse spatial and temporal data‐sets, resulting in a degree of uncertainty in their conclusions. Furthermore, previous methodologies have been unable to quantify small‐scale changes in channels composed of sand and fine gravel due to inadequate data density. This study reports the use of a high‐resolution 3D laser scanner (LMS‐Z210) in the assessment of erosion and deposition volumes in the proglacial zone of Glacier du Ferpècle and Mont Miné, Switzerland. High‐resolution (>500 points/m2) data obtained across a 5881 m2 area of braid plain during the early part of the melt‐water season permitted digital elevation models (DEMs) of bar surfaces and channels to be produced. The approach negates the need for complex surface interpolation algorithms required in surveys with lower point density, e.g. those obtained from global positioning systems or total stations. Furthermore, the technique has the advantage of being able to cover a large area over a comparatively short time period. Laser scanner returns revealed high vertical precision, ±0·02 m, for dry bar surfaces; however, submerged areas (<0·2 m depth) returned lower precision, with a range of −0·15 to +0·06 m. To account for this, different levels of detection (LoD) were applied to the dry and wet parts of the study reach during DEM subtraction. Subtraction of successive DEMs revealed two short depositional episodes over the ten‐day study, with erosion dominating in between. Three episodes of avulsion were identified, two of which appeared to be triggered by constriction avulsion, whilst the other was initiated by bar‐edge erosion. Transient lobes and sediment sheets could also be identified at the downstream end of the reach, as could lobe progradation. Relatively minor, but common, changes in channel morphology could also be detected, such as bar edge accretion, bank erosion and chute development. In an analysis of the effects of survey frequency upon volumes calculated following DEM subtraction, daily surveys were found to increase erosion volumes by 67 per cent and deposition volumes by 14 per cent when compared with an 8‐day survey interval. Copyright © 2007 John Wiley & Sons, Ltd.
Nucleotide sequence of an intronless gene for a human arylamine N-acetyltransferase related to polymorphic drug acetylation.

A genetic polymorphism of liver arylamine N-acetyltransferase (NAT; EC 2.3.1.5) activity in man causes interindividual variation in the response to a variety of amine drugs and potential carcinogens (1). We screened a human XEMBL3 genomic library, constructed using DNA from a heterozygous rapid acetylator, using a cDNA specific for rabbit liver NAT (2). Below is shown the complete nucleotide sequence of a 1891 bp EcoRI fragment from one of the positive clones which contains an open reading frame with the potential to encode a human NAT. The gene contains no introns and shows 82% and 61% homology in the coding region to cDNAs for rabbit (2) and chicken (3) liver NAT, respectively. The fragment was expressed using the SV40-based vector p91023(B) in COS-1 cells to produce a protein with enzyme activity characteristic of a genetically polymorphic human NAT (4).