Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of two parallel intruders on total work during granular penetrations

Swapnil Pravin ,1,*,† Brian Chang ,1,† Endao Han ,2,‡ Lionel London ,3 Daniel I. Goldman,4 Heinrich M. Jaeger,2 and S. Tonia Hsieh 1,§ 1Department of Biology, Temple University, Philadelphia, Pennsylvania 19122, USA 2James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA 3Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA 4Georgia Institute of Technology, Atlanta, Georgia 30332, USA
Measurement of surface water runoff from plots of two different sizes

Intensities and amounts of water infiltration and runoff on sloping land are governed by the rainfall pattern and soil hydraulic conductivity, as well as by the microtopography and soil surface conditions. These components are closely interrelated and occur simultaneously, and their particular contribution may change during a rainfall event, or their effects may vary at different field scales. The scale effect on the process of infiltration/runoff was studied under natural field and rainfall conditions for two plot sizes: small plots of 0·25 m2 and large plots of 50 m2. The measurements were carried out in the central region of Chile in a piedmont most recently used as natural pastureland. Three blocks, each having one large plot and five small plots, were established. Cumulative rainfall and runoff quantities were sampled every 5 min. Significant variations in runoff responses to rainfall rates were found for the two plot sizes. On average, large plots yielded only 40% of runoff quantities produced on small plots per unit area. This difference between plot sizes was observed even during periods of continuous runoff. Copyright © 2002 John Wiley & Sons, Ltd.
The Malari leucogranite, Garhwal Himalaya, northern India: Chemistry, age, and tectonic implications

In the Garhwal region, India, the Malari leucogranite cuts the South Tibetan detachment system, a large-scale normal fault system at the top of the High Himalaya. The leucogranite crosscuts ductile normal-sense shear fabrics and has experienced relatively little subsolidus brittle deformation or alteration. Its relatively evolved bulk chemical composition, high Rb/Sr ratio, and normative corundum indicate a (meta)sedimentary source, likely the underlying Greater Himalayan sequence. Zircon U-Pb ages, collected by laser-ablation inductively coupled plasma–mass spectrometry (ICP-MS) and corrected for initial U/Th disequilibrium, indicate emplacement at 19.0 ± 0.5 Ma. Thus, ductile normal shear on the South Tibetan detachment system must have ceased by 19 Ma. Studies elsewhere in the Himalaya suggest initiation of South Tibetan detachment system ductile movement not earlier than 24 Ma, and likely ca. 22 Ma. The short duration of extension (≤5 and likely ∼3 m.y.) and early cessation contrast with channel-flow models that predict long-duration ductile normal shear, and large displacements after ca. 20 Ma. Observations are instead better explained by critical taper models, in which internal weakening of the wedge, likely from partial melting, caused a brief interval of flattening and ductile extension in the rear of the wedge.
Low intensity of the geomagnetic field in Early Jurassic time

From a large collection of Jurassic continental tholeiites cropping out in Europe and Africa, we selected 90 samples for paleointensity determinations. The samples were carefully selected to avoid any secondary magnetizations, especially viscous magnetization. Use of the Thellier method reveals that magnetic property changes due to heating begin often at quite low temperatures but fortunately without modifying noticeably their natural remanent magnetization-thermoremanent magnetization ratio. Twenty-eight well-clustered paleointensity estimates were obtained from two European dikes that were emplaced during Early Jurassic time: the Kerforne dike at Brenterc'h in Brittany (northwestern France) and the Messejana dike on the Iberian Peninsula (Spain and Portugal). Virtual dipole moments calculated from both magmatic units are similar and only about one-third of present-day values. These new data lend support to the recently postulated low dipole moment of the Mesozoic geomagnetic field.
Possible concurrence of TDP‐43, tau and other proteins in amyotrophic lateral sclerosis/frontotemporal lobar degeneration

Transactivation response DNA‐binding protein 43 kDa (TDP‐43) has been regarded as a major component of ubiquitin‐positive/tau‐negative inclusions of motor neurons and the frontotemporal cortices in amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD). Neurofibrillary tangles (NFT), an example of tau‐positive inclusions, are biochemically and morphologically distinguished from TDP‐43‐positive inclusions, and are one of the pathological core features of Alzheimer disease (AD). Although ALS/FTLD and AD are distinct clinical entities, they can coexist in an individual patient. Whether concurrence of ALS/FTLD‐TDP‐43 and AD‐tau is incidental is still controversial, because aging is a common risk factor for ALS/FTLD and AD development. Indeed, it remains unclear whether the pathogenesis of ALS/FTLD is a direct causal link to tau accumulation. Recent studies suggested that AD pathogenesis could cause the accumulation of TDP‐43, while abnormal TDP‐43 accumulation could also lead to abnormal tau expression. Overlapping presence of TDP‐43 and tau, when observed in a brain during autopsy, should attract attention, and should initiate the search for the pathological substrate for this abnormal protein accumulation. In addition to tau, other proteins including α‐synuclein and amyloid β should be also taken into account as candidates for an interaction with TDP‐43. Awareness of a possible comorbidity between TDP‐43, tau and other proteins in patients with ALS/FTLD will be useful for our understanding of the influence of these proteins on the disease development and its clinical manifestation.
Temperature independence of carbon dioxide supersaturation in global lakes

A growing body of evidence suggests that most of the world's lakes are supersaturated with CO2 and export significant amounts of CO2 to the atmosphere. Still, the temperature dependence of the partial pressure of CO2 (pCO2) in lakes, which is the main driver of carbon flux across the air‐water interface, has not yet been assessed. Analyzing a global‐scale database of 4902 lakes, we show that temperature is not an important regulator of pCO2 in lakes. Instead, the concentration of dissolved organic carbon (DOC), a substrate for microbial respiration, explains significant variation in lake pCO2. Contrary to what may be expected from the physiological constraints of temperature, effects of climate change on the carbon balance of lakes may not be due to rising temperature per se, but rather to climatically induced changes in the export of DOC from terrestrial soils to aquatic habitats.
Post‐collisional granite generation and HT–LP metamorphism by radiogenic heating: the Variscan South Bohemian Batholith

The Palaeozoic Variscan Orogen of Europe is a well‐documented example of a collision zone characterized by widespread late‐orogenic high‐temperature metamorphism and associated crustal magmatism. However, the heat source is still under debate. Based on the Bohemian Massif in the internal zone of the Variscides as case study, we present geological, geochemical, petrological and geochronological data arguing against a substantial mantle involvement in metamorphism and magma genesis in the area of the South Bohemian Batholith. In order to provide an alternative explanation consistent with heat transfer mechanism, we apply a two‐dimensional thermal–kinematic modelling approach. The model calculates the transient lithospheric temperature field during crustal thickening and subsequent thinning by erosiorf from material parameters and boundary conditions specific to the study area. Model results show that the increased contribution of radiogenic heat in the thickened crust can indeed cause a substantial temperature increase in the middle and lower crust. Model predictions are in good agreement with observations, e.g. the P–T–t evolution of the country rocks, the formation of syn‐kinematic migmatites, the large volumes of peraluminous granites derived from dehydration melting of metasediments and the small volumes of lamprophyric melts from the mantle lithosphere. The results of this study emphasize the importance of radiogenic heat as the source for high‐temperature metamorphism and granite petrogenesis in the Bohemian Massif and potentially in other areas of the Variscan Orogen.
Linking channel hydrology with riparian wetland accretion in tidal rivers

The hydrologic processes by which tide affects river channel and riparian morphology within the tidal freshwater zone are poorly understood yet are fundamental to predicting the fate of coastal rivers and wetlands as sea level rises. We investigated patterns of sediment accretion in riparian wetlands along the nontidal through oligohaline portion of two coastal plain rivers in Maryland, U.S., and how flow velocity, water level, and suspended sediment concentration (SSC) in the channel may have contributed to those patterns. Sediment accretion was measured over a 1 year period using artificial marker horizons, channel hydrology was measured over a 1 month period using acoustic Doppler current profilers, and SSC was predicted from acoustic backscatter. Riparian sediment accretion was lowest at the nontidal sites (mean and standard deviation = 8 ± 8 mm yr−1), highest at the upstream tidal freshwater forested wetlands (TFFW) (33 ± 28 mm yr−1), low at the midstream TFFW (12 ± 9 mm yr−1), and high at the oligohaline (fresh‐to‐brackish) marshes (19 ± 8 mm yr−1). Channel maximum flood and ebb velocity was twofold faster at the oligohaline than tidal freshwater zone on both tidal rivers, corresponding with the differences in in‐channel SSC: The oligohaline zone's SSC was more than double the tidal freshwater zone's and was greater than historical SSC at the nontidal gages. The tidal wave characteristics differed between rivers, leading to significantly greater in‐channel SSC during floodplain inundation in the weakly convergent than the strongly convergent tidal river. High sediment accretion at the upstream TFFW was likely due to high river discharge following a hurricane.
Explaining the colour of power spectra in chaotic ecological models

Power spectrum analysis is often used to determine whether population time series are dominated by particular frequencies. Results for chaotic time series are often reported in terms of the colour of the spectra whereby red spectra indicate a dominance of low frequency (long-term) fluctuations, white spectra indicate that all frequencies are equally dominant and blue spectra indicate a dominance of high frequency (short-term) fluctuations. Several studies have employed such analysis and much discussion has been provoked by an apparent conflict between the fact that the time series of natural populations produce reddened power spectra whereas chaotic, single species ecological models can produce blue, white or red spectra. Here, we resolve the question of which parameter values give rise to particular colour spectra by analysing simple models in terms of ‘universal’ parameters allowing direct comparisons between models to be drawn. This suggests that some models are not capable of producing reddened spectra, which would question their usefulness in describing ecological systems. The population behaviour associated with each colour spectrum is described and compared with models that incorporate simple modifications to represent delayed density dependence, spatial structure and environmental effects.
Order and Chaos: NTK views on DNN Normalization, Checkerboard and Boundary Artifacts

We analyze architectural features of Deep Neural Networks (DNNs) using the so-called Neural Tangent Kernel (NTK), which describes the training and generalization of DNNs in the infinite-width setting. In this setting, we show that for fully-connected DNNs, as the depth grows, two regimes appear: "order", where the (scaled) NTK converges to a constant, and "chaos", where it converges to a Kronecker delta. Extreme order slows down training while extreme chaos hinders generalization. Using the scaled ReLU as a nonlinearity, we end up in the ordered regime. In contrast, Layer Normalization brings the network into the chaotic regime. We observe a similar effect for Batch Normalization (BN) applied after the last nonlinearity. We uncover the same order and chaos modes in Deep Deconvolutional Networks (DC-NNs). Our analysis explains the appearance of so-called checkerboard patterns and border artifacts. Moving the network into the chaotic regime prevents checkerboard patterns; we propose a graph-based parametrization which eliminates border artifacts; finally, we introduce a new layer-dependent learning rate to improve the convergence of DC-NNs. We illustrate our findings on DCGANs: the ordered regime leads to a collapse of the generator to a checkerboard mode, which can be avoided by tuning the nonlinearity to reach the chaotic regime. As a result, we are able to obtain good quality samples for DCGANs without BN.
Standardised measurements used to order compression garments can be used to calculate arm volumes to evaluate lymphoedema treatment

Abstract Lymphoedema treatment outcome can be evaluated by calculating estimated limb volumes directly by water displacement (plethysmography; PG), or indirectly by circumference measurements (CM) and using the formula for a truncated cone. This study assessed the correlation between PG and circumference volume measurements to assess whether the correlation is acceptable, and if circumference measurements can be used to accurately assess arm volume. Ten women with unilateral lymphoedema after breast cancer treatment with a mean age of 66 (range 50–83) years volunteered for arm volume estimates by PG and circumference measurements. The coefficient of variation (CV%) for all methods was calculated. Two Excel-based formulae of the truncated cone were developed; one for fixed 4-cm intervals leading to 10 volume segments (CM-10-VS), and one for varying intervals leading to four volume segments (CM-4-VS). The CV% was 0.609% for PG, 0.628% for CM-10-VS, and 0.632% for CM-4-VS. As expected, PG generated a significantly larger volume of both arms because it includes the hand. The difference between CM-10-VS and CM-4-VS measurements was not significant. All three measurement methods showed a high coefficient of correlation (0.813–0.915), and a high coefficient of regression (0.863–1.089). The excess volume, which is used to determine treatment outcome, showed the respective values of 0.932–0.978 and 0.963–1.020, respectively. Using circumference measurements identical to those used when ordering made-to-measure compression garments speeds up volume measurements and can be used safely to evaluate lymphoedema treatment outcome.
Greenland ice sheet elevation change since 1978 from radar and laser altimetry 1

Abstract Repeat satellite radar altimetry gives estimates of surface elevation change for the southern half of the Greenland ice sheet between 1978 and 1988, and repeat aircraft laser altimetry gives equivalent estimates for 1993–1998. Over large areas away from the coast, the two data sets show the ice sheet to be in balance, but with localized zones of significant thickening or thinning. Rates of surface elevation change derived by comparing localized 1980 ground surveys with 1993–1994 laser surveys show excellent agreement with the 1978–1988 radar results, suggesting that the radar altimeter provides reliable estimates of elevation change when data are averaged over areas of ice sheet with low surface slopes. Regions where there are significant differences between the 1978–1988 and 1993–1998 results can be explained either by changes in near‐surface snow conditions that affect the radar reflecting horizon, or by temporal variability in snow accumulation rates.
Intestinal stem cell differentiation is associated with dynamic changes in the chromatin landscape

Chromatin is central to cellular identity and is remodeled as stem cells differentiate and acquire mature cell fates. In the adult intestinal epithelium, functional plasticity facilitates de-differentiation and reacquisition of stemness by progenitors and some post-mitotic cell types following damage to the intestinal stem cell (ISC) pool. Previous studies have suggested that this plasticity is regulated by largely homogenous or “static” chromatin landscapes shared by ISCs and their progeny. Here, we utilize a Sox9 EGFP reporter mouse to examine native chromatin across the continuum of ISC differentiation. Our data reveal a highly dynamic chromatin landscape in IECs, associated mainly with open chromatin regions (OCRs) found in intergenic or intragenic loci consistent with putative distal enhancers. By integrating gene expression with chromatin accessibility at transcription factor (TF) binding motifs in context of Sox9 EGFP populations, we classify “static” and “dynamic” chromatin relative to specific TF usage. These analyses identify known and potential regulators of ISC differentiation via their association with dynamic changes in chromatin and suggest that differential cis - and trans -regulatory significance can be defined in a locus-specific manner. Finally, we apply the Sox9 EGFP model to examine the relationship between gene expression which reveals a role for 5hmC in absorptive lineage specification. Together, our data demonstrate a previously unappreciated degree of global chromatin changes in intestinal epithelial cells (IECs), identify novel potential regulators of ISC differentiation, and provide a chromatin roadmap for further dissecting the role of cis regulation of cell fate in the intestine.
Mechanistic Heterogeneity in Contractile Properties of (cid:2) -Tropomyosin ( TPM1 ) Mutants Associated with Inherited Cardiomyopathies *

Background: Single residue substitutions in sarcomeric proteins cause most inherited cardiomyopathies. Results: Mutant (cid:2) -tropomyosins cause multiple functional alterations in actin affinity and Ca 2 (cid:2) sensitivity. Conclusion: Mutants follow distinct mechanisms to change Ca 2 (cid:2) sensitivity. Significance: Fluorescence assays to measure changes in troponin C conformation may provide a simple platform for prelim-inary high throughput screening of modulatory small molecules to treat inherited cardiomyopathies. proteins. Amongthoseare30single-residuemutationsin TPM1 ,thegene encoding (cid:2) -tropomyosin. We examined seven mutant tropo-myosins, E62Q, D84N, I172T, L185R, S215L, D230N, and M281T, that were chosen based on their clinical severity and locations along the molecule. The goal of our study was to determine how the biochemical characteristics of each of these mutantproteinsarealtered,whichinturncouldprovideastruc-tural rationale for treatment of the cardiomyopathies they produce. Measurements of Ca 2 (cid:3) sensitivity of human (cid:4) -cardiac myosin ATPase activity are consistent with the hypothesis that hypertrophic cardiomyopathies are hypersensitive to Ca 2 (cid:3) acti-vation,anddilatedcardiomyopathiesarehyposensitive.Wealso report correlations between ATPase activity at maximum Ca 2 (cid:3) concentrations and conformational changes in TnC measured using a fluorescent probe, which provide evidence that different substitutions perturb the structure of the regulatory complex in different ways. Moreover, we observed changes in protein stability and protein-protein interactions in these mutants. Our results suggest multiple mechanistic pathways to hypertrophic and dilated cardiomyopathies. Finally, we examined a computa-tionally designed mutant, E181K, that is hypersensitive, con-firming predictions derived from in silico structural analysis.
Morphological patterns of Aptian Lithocodium–Bacinella geobodies: relation to environment and scale

Lithocodium aggregatum and Bacinella irregularis are now extinct, shallow marine life forms of unknown taxonomic origin. Forming part of the tropical platform biota during much of the Mesozoic, these organisms experienced bloom periods and temporarily replaced rudist–coral assemblages during parts of the Early Aptian. Within the limitations of time resolution, this ‘out‐of‐balance’ facies is coeval with the Oceanic Anoxic Event 1a‐related black shale deposition in oceanic basins but the triggering factors remain poorly understood. Here, a platform‐wide comparison of Lithocodium–Bacinella geobodies and morphotypes from the Sultanate of Oman is presented and placed in its environmental, bathymetric and physiographic context. Lithocodium–Bacinella geobodies reach from kilometre‐scale ‘superstructures’ to delicate centimetre‐sized growth forms. Clearly, scale matters and care must be taken when drawing conclusions based on spatially limited observational data. Whilst the factors that cause Lithocodium–Bacinella expansion should probably be considered in a global context, regional to local factors affected growth patterns in a more predictable manner. Here, the unresolved taxonomic relationship remains the main obstacle in any attempt to unravel the response of Lithocodium–Bacinella to specific or interlinked environmental parameters as different organisms respond differently to changing environment. Acknowledging these limitations, the following tentative patterns are observed: (i) Lithocodium–Bacinella tolerated a wide range of hydrodynamic levels and responded to differences in energy level or physiographic settings (margin, intrashelf basin, inner platform) by obtaining characteristic growth forms. (ii) Lithocodium–Bacinella favoured low‐sediment input but had the ability to react to higher sedimentation rates by enhanced upward growth; a feature perhaps pointing to a phototrophic metabolism. Circumstantial evidence for continuous growth within the upper‐sediment column is debated. (iii) The availability of accommodation space had a direct influence on the maximum size of geobodies formed. (iv) Fluctuating nutrient levels and sea water alkalinity may have affected the growth potential of Lithocodium–Bacinella. Understanding the relationship between Lithocodium–Bacinella morphogenesis on a wide range of scales and local environmental parameters allows for better prediction of the spatial distribution of reservoir properties and also results in an improved interpretation of palaeoenvironments. This study might represent a useful first step in this direction.