Miracle-dz/UniFAR-FTUs huggingface dataset:
The sensitivity of a GCM's marine stratocumulus to cloud‐top entrainment

It appears that the Met Office general‐circulation model (GCM) represents stratocumulus over the northeast subtropical Pacific Ocean quite accurately—the mean cloud cover is realistically high, the observed mean and diurnal cycle of liquid‐water path is well represented and the capping inversion is at a reasonable height. This suggests that the boundary‐layer thermodynamic budget must also be well modelled. However, one of the dominant terms in this budget is cloud‐top entrainment, which is parametrized explicitly in this model, and is still the subject of much debate in the literature. In order to quantify the sensitivity of the GCM to this parametrization, the results of simulations applying three perturbations of entrainment formulation are presented. One change, to the enhancement of entrainment in the buoyancy‐reversal regime, is found to have little impact. The other two led to a significant reduction of the cloudiness in the stratocumulus area, giving worse agreement with observations. The first of these was to increase the parametrized entrainment rate by a factor of two. The second was to remove the coupling of the entrainment fluxes to the radiative and resolved advective fluxes, an aspect of the implementation previously found necessary to prevent serious numerical errors which generated spurious additional entrainment. It is further hypothesized that the numerical errors can be associated with a signal in the surface heat fluxes in the north‐east Pacific stratocumulus area. This signal can be seen in many other GCMs, suggesting that numerical problems associated with mixing across sharp inversions may be prevalent. © Crown copyright, 2004.
The optical properties of mica in the vacuum ultraviolet

Optical reflection and transmission measurements have been made between 6 eV and 13 eV on specimens of natural muscovite, phlogopite, biotite and a synthetic fluorphlogopite. Reflectivity peaks are observed near 9.9 eV and 11.8 eV and are thought to be due to the silicate structure of mica. An absorption edge occurs near 7.85 eV in synthetic mica. Additional structure is observed above 7.8 eV in the magnesium micas but not in the aluminium micas. The absorption of phlogopite mica is unusually low in the high energy region. Below 7.8 eV absorption is believed to depend on transition metal impurities in the mica.
Heat stress conditions affect the social network structure of free‐ranging sheep

Extreme weather conditions, like heatwave events, are becoming more frequent with climate change. Animals often modify their behaviour to cope with environmental changes and extremes. If the environmental conditions influence the trade-off between an individual’s social propensity and optimal thermoregulation through shade use for instance, then divergent social decisions may be made. Hence, such behavioural changes have the potential to influence an individual’s position in its social network, and the social network structure as a whole. We investigated whether heat stress conditions (quantified through the Temperature Humidity Index) and the resulting use of shaded areas, influences the social network structure and an individual’s position in it. We studied this in free-ranging sheep in the arid zone of Australia, GPS-tracking all 48 individuals in a flock. When heat stress conditions worsened, individuals spent more time in the shade and the network was more connected (higher density) and less modular. Furthermore, an individual’s social connectivity scaled with its shade use behaviour. Interestingly, individuals with intermediate shade use were most strongly connected (degree, strength, betweeness), indicating their importance for the connectivity of the social network during heat stress conditions. Our study shows that heat stress conditions, which are predicted to increase in severity and frequency due to climate change, influence the resource use within the ecological environment. This has flow on effects for the animal’s social environment through the changed social network structure. Significance statement Due to climate change, animals experience heat stress conditions more frequently. When ambient temperatures are high, individuals can seek shaded areas to mitigate the effect. However, whether these behavioural changes affect the interaction patterns in social species is not well understood. We tracked all individuals in a flock of sheep using GPS collars. We demonstrate that when heat stress conditions worsened (higher temperature humidity index), individuals spent more time in the shade and the social network was more connected with less internal structure. Furthermore, an individual’s social connectivity scaled with its shade use behaviour, and individuals with intermediate shade use were most strongly connected in their social network. Our findings illustrate that individuals respond to climate change induced environmental conditions and that this has flow on effects for their social connectivity and the social network of the group.
Cyclic peptide structure prediction and design using AlphaFold

Deep learning networks offer considerable opportunities for accurate structure prediction and design of biomolecules. While cyclic peptides have gained significant traction as a therapeutic modality, developing deep learning methods for designing such peptides has been slow, mostly due to the small number of available structures for molecules in this size range. Here, we report approaches to modify the AlphaFold network for accurate structure prediction and design of cyclic peptides. Our results show this approach can accurately predict the structures of native cyclic peptides from a single sequence, with 36 out of 49 cases predicted with high confidence (pLDDT > 0.85) matching the native structure with root mean squared deviation (RMSD) less than 1.5 Å. Further extending our approach, we describe computational methods for designing sequences of peptide backbones generated by other backbone sampling methods and for de novo design of new macrocyclic peptides. We extensively sampled the structural diversity of cyclic peptides between 7–13 amino acids, and identified around 10,000 unique design candidates predicted to fold into the designed structures with high confidence. X-ray crystal structures for seven sequences with diverse sizes and structures designed by our approach match very closely with the design models (root mean squared deviation < 1.0 Å), highlighting the atomic level accuracy in our approach. The computational methods and scaffolds developed here provide the basis for custom-designing peptides for targeted therapeutic applications.
luxA gene from Enhygromyxa salina encodes a functional homodimeric luciferase

Several clades of luminescent bacteria are known currently. They all contain similar lux operons, which include the genes luxA and luxB encoding a heterodimeric luciferase. The aldehyde oxygenation reaction is catalyzed by the subunit LuxA, while LuxB is inactive. Recently, genomic analysis identified a subset of bacterial species with rearranged lux operons lacking luxB. Here, we show that Escherichia coli transformed with a synthetic luxA gene from the reduced luxACDE operon of Enhygromyxa salina is luminescent upon addition of aldehydes. Overall, EsLuxA is less bright compared to luciferases from Aliivibrio fischeri (AfLuxAB) and Photorhabdus luminescens (PlLuxAB), and most active with medium-chain C4-C9 aldehydes. Crystal structure of EsLuxA determined at the resolution of 2.71 Å reveals a classical monooxygenase fold, and the protein preferentially forms a dimer in solution. The mobile loop residues 264-293, which form a β-hairpin or a coil in Vibrio harveyi LuxA, form α-helices in EsLuxA. Phylogenetic analysis shows EsLuxA and related proteins may be bacterial protoluciferases that arose prior to duplication of the luxA gene and its speciation to luxA and luxB in the previously described luminescent bacteria. Our work paves the way for discovery of new luciferases that have an advantage of being encoded by a single gene.
A necessary condition for the geodynamo

A necessary condition for the generation of magnetic fields by fluid motions in a sphere is derived in terms of the magnetic Reynolds number on the basis of the radial component of the velocity field. A second parameter entering the criterion is the ratio between the energy of the poloidal component of the magnetic field and the total magnetic energy. Since bounds on this ratio can be obtained from energetic considerations, the criterion can be used as a restriction on possible dynamo mechanisms. Several recent suggestions for the origin of the geodynamo in a stratified outer core are critically reviewed.
On TLS for the Internet of Things, in a Post Quantum world

The TLS (Transport Layer Security) protocol is the most important, most attacked, most analysed and most used cryptographic protocol in the world today. TLS is critical to the integrity of the Internet, and if it were to be broken e-commerce would become impossible, with very serious implications for the global economy. Furthermore TLS is likely to assume even greater significance in the near future with the rapid growth of an Internet of Things (IoT) – a multiplicity of internet connected devices all engaged in secure inter-communication. However the impending invention of a Cryptographically Relevant Quantum Computer (CRQC) would represent an existential threat to TLS in its current form. As it stands the latest version TLS1.3, benefiting as it does from years of research and study, provides effective security, but it must soon be updated to resist this new threat. In this research we first under-take a new clean-room implementation of a small-footprint open source TLS1.3, written in C ++ and Rust, and suitable for IoT applications. Our implementation is designed to be cryptographically agile, so that it can easily accomodate new post-quantum cryptographic primitives. Next we use this new implementation as a vehicle to study the impact of going post-quantum, with a particular emphasis on the impact on the Internet of Things. Finally we showcase the flexibility of our implementation by proposing an implementation of TLS that uses identity-based encryption to mitigate this impact.
QCD running coupling in low-energy region

We estimate the QCD effective charge {alpha}{sub s} in the low-energy region by exploiting the conventional meson spectrum within a relativistic quantum-field model based on analytic confinement. The ladder Bethe-Salpeter equation is solved for the masses of two-quark bound states. We found a new, independent, and specific infrared-finite behavior of QCD coupling below energy scale 1 GeV. Particularly, an infrared-fixed point is extracted at {alpha}{sub s}(0){approx_equal}0.757 for confinement scale {Lambda}=345 MeV. As an application, we estimate masses of some intermediate and heavy mesons and obtain results in reasonable agreement with recent experimental data.
Antithrombin III and Heparin Cofactor II in Patients with Chronic Renal Failure Undergoing Regular Hemodialysis

Summary Heparin enhances the inhibition rate of thrombin by both antithrombin III (AT III) and heparin cofactor II (HC II). We studied the activity of these two plasma proteins in patients with chronic renal failure (CRF) undergoing regular hemodialysis as their heparin requirements varied widely. In 77 normal blood donors, normal ranges (mean ± 2 SD) were 82-122% for AT III and 65-145% for HC II. When compared with these controls 82 dialyzed CRF patients had a subnormal AT III activity and a significantly (p <0.001) lower HC II activity. To evaluate the effect of hemodialysis we compared AT III, HC II and total proteins in plasma before and after dialysis in. 24 patients (12 with normal and 12 with low basal HC II activity). AT III and HC II activities significantly (p <0.001) increased in absolute value. When related to total plasma proteins, in order to suppress the influence of hemoconcentration induced by dialysis, AT III decreased significantly (p <0.01) whereas HC II increased slightly but significantly (p <0.01) in the 12 patients with low initial HC II activity. The decrease of AT III induced by heparin administrated during dialysis is likely to account for this relative decrease of AT III activity. A modification of the distribution of both HC II and heparin between the vascular wall and the circulating blood is evoked to explain the relative increase in HC II activity and the need for higher heparin dosage in patients with low HC II levels.
Verifiable Distributed Aggregation Functions

The modern Internet is built on systems that incentivize collection of information about users. In order to minimize privacy loss, it is desirable to prevent these systems from collecting more information than is required for the application. The promise of multi-party computation is that data can be aggregated without revealing individual measurements to the data collector. This work offers a provable security treatment for "Verifiable Distributed Aggregation Functions (VDAFs)", a class of multi-party computation protocols being considered for standardization by the IETF. We propose a formal framework for the analysis of VDAFs and apply it to two constructions. The first is Prio3, one of the candidates for standardization. This VDAF is based on the Prio system of Corrigan-Gibbs and Boneh (NSDI 2017). We prove that Prio3 achieves our security goals with only minor changes to the draft. The second construction, called Doplar, is introduced by this paper. Doplar is a round-reduced variant of the Poplar system of Boneh et al. (IEEE S&P 2021), itself a candidate for standardization. The cost of this improvement is a modest increase in overall bandwidth and computation.
A study of inter-crystal scatter in small scintillator arrays designed for high resolution PET imaging

Inter-crystal scatter causes mispositioning of scintillation events, which is of particular concern in imaging detectors based on small discrete scintillators. Because it is difficult to measure the scatter and its effects on detector intrinsic spatial resolution, a Monte Carlo simulation has been used to study this effect for evaluating and optimizing the design of a high resolution animal PET detector based on a small scintillator crystal array. In this simulation, the authors quantitatively assess the mispositioning of events due to inter-crystal scatter as a function of parameters such as different scintillator materials, crystal geometry, /spl gamma/-ray incident angle and energy threshold applied, etc. In analyzing the tradeoff between the detector efficiency and the position detection accuracy, the authors found that the mispositioning is not sensitive to the energy threshold, however it does change rapidly with the crystal length and the gap between crystals. The authors also evaluated different crystal positioning schemes to provide a theoretical estimation for the choice of the best scheme. To study how the inter-crystal scatter affects detector spatial resolution, the authors analyze the coincidence line spread function with and without the scatter, and found that the inter-crystal scatter has very little effect on the FWHM and FWTM of the coincidence line spread function.
Verifiable Multi-Client Functional Encryption for Inner Product

Joint computation on encrypted data is becoming increasingly crucial with the rise of cloud computing. In theory, multi-party computation (MPC) allows for secure computation, but it is often impractical due to intensive interactions between users. In recent years, the development of multi-client functional encryption (MCFE) has made it possible to perform joint computation on private inputs, without any interaction. Well-settled solutions for linear functions have become eﬃcient and secure, but there is still a shortcoming: if one user inputs incorrect data, the output of the function might become meaningless for all other users (while still useful for the malicious user). To address this issue, the concept of veriﬁable functional encryption was introduced by Badrinarayanan et al. at Asiacrypt ’16 (BGJS). However, their solution was impractical because of strong statistical requirements. More recently, Bell et al. introduced a related concept for secure aggregation, with their ACORN solution, but it requires multiple rounds of interactions between users. In this paper, – we ﬁrst propose a computational deﬁnition of veriﬁability for MCFE. Our notion covers the computational version of BGJS and extends it to handle any valid inputs deﬁned by predicates. The BGJS notion corresponds to the particular case of a ﬁxed predicate, in our setting. – we then design a concrete construction of veriﬁable MCFE for inner-product computations where the inputs are within a range. Veriﬁability cannot be easily obtained from classical proof systems only because the encryption key is usually secret in MCFE and the encryptor can maliciously perform the encryption without being detected. So we need to eﬀectively combine diﬀerent techniques such as commitments and range proofs to achieve the veriﬁability. Our approach can also be applied to input validation for secure aggregation as a special case.
On the speed of convergence to equilibrium states for multi-dimensional maps with indifferent periodic points

We shall clarify the speed of L1-convergence of iterated transfer operators and rates of decay of correlations for multi-dimensional noninvertible maps with indifferent periodic points related to a class of functions which contains all piecewise Lipschitz functions. The essential issue for solving these problems is to clarify the speed of uniform convergence of transfer operators on compact sets excluding indifferent periodic points. Our results can be applicable to higher dimensional countable to one intermittent maps for which previous techniques on decay of correlations do not work.
B, V PHOTOMETRY FOR ∼19,000 STARS IN AND AROUND THE MAGELLANIC CLOUD GLOBULAR CLUSTERS NGC 1466, NGC 1841, NGC 2210, NGC 2257, AND RETICULUM

Homogeneous B, V photometry is presented for 19,324 stars in and around 5 Magellanic Cloud globular clusters: NGC 1466, NGC 1841, NGC 2210, NGC 2257, and Reticulum. The photometry is derived from eight nights of CCD imaging with the Cerro Tololo Inter-American Observatory 0.9 m SMARTS telescope. Instrumental magnitudes were transformed to the Johnson B, V system using accurate calibration relations based on a large sample of Landolt–Stetson equatorial standard stars, which were observed on the same nights as the cluster stars. Residual analysis of the equatorial standards used for the calibration, and validation of the new photometry using Stetson's sample of secondary standards in the vicinities of the five Large Magellanic Cloud clusters, shows excellent agreement with our values in both magnitudes and colors. Color–magnitude diagrams reaching to the main-sequence turnoffs at V ∼ 22 mag, sigma–magnitude diagrams, and various other summaries are presented for each cluster to illustrate the range and quality of the new photometry. The photometry should prove useful for future studies of the Magellanic Cloud globular clusters, particularly studies of their variable stars.
Amazonian Deforestation: Impact of Global Warming on the Energy Balance and Climate

AbstractA coupled biosphere–atmosphere statistical–dynamical model is used to study the relative roles of the impact of the land change caused by tropical deforestation and global warming on energy balance and climate. Three experiments were made: 1) deforestation, 2) deforestation + 2 × CO2, and 3) deforestation + CO2, CH4, N2O, and O3 for 2100. In experiment 1, the climatic impact of the Amazonian deforestation is studied. In experiment 2, the effect of doubling CO2 is included. In experiment 3, the concentrations of the greenhouse gases (GHGs) correspond to the A1FI scenario from the Intergovernmental Panel on Climate Change Special Report on Emissions Scenarios. The results showed that the percentage of the warming caused by deforestation relative to the warming when the increase in GHG concentrations is included is higher than 60% in the tropical region. On the other hand, with the increase in GHG concentrations, a reduction in the decrease of evapotranspiration and precipitation in the tropical regi.
Direct numerical simulation of free falling sphere in creeping flow

In the present study, direct numerical simulations (DNS) are performed on single and a swarm of particles settling under the action of gravity. The simulations have been carried out in the creeping flow range of Reynolds number from 0.01 to 1 for understanding the hindrance effect, of the other particles, on the settling velocity and drag coefficient. The DNS code is a non-Lagrange multiplier-based fictitious-domain method, which has been developed and validated by Jin et al. (2008; A parallel algorithm for the direct numerical simulation of 3D inertial particle sedimentation. In: Conference proceedings of the 16th annual conference of the CFD Society of Canada). It has been observed that the time averaged settling velocity of the particle in the presence of other particles, decreases with an increase in the number of particles surrounding it (from 9 particles to 245 particles). The effect of the particle volume fraction on the drag coefficient has also been studied and it has been observed that the computed values of drag coefficients are in good agreement with the correlations proposed by Richardson and Zaki (1954; Sedimentation and fluidization: part I. Transactions of the Institution of Chemical Engineers, 32, 35–53) and Pandit and Joshi (1998; Pressure drop in packed, expanded and fluidised beds, packed columns and static mixers – a unified approach. Reviews in Chemical Engineering, 14, 321–371). The suspension viscosity-based model of Frankel and Acrivos (1967; On the viscosity of a concentrated suspension of solid spheres. Chemical Engineering Science, 22, 847–853) shows good agreement with the DNS results.
Measurement of the \(W^{\pm}Z\) Production Cross Section and Limits on Anomalous Triple Gauge Couplings at \(\sqrt s = 7 TeV\) using the ATLAS detector

This dissertation presents a measurement of the W±Z production cross section and limits on anomalous triple gauge couplings in proton-proton collisions at a center of mass energy of 7 TeV using data produced by LHC collisions and acquired by the ATLAS detector in 2011. The measurement and limits probe the electroweak sector of the Standard Model at high energies and allow for generic tests for new physics that could be present at high energy scales. This analysis is also useful for understanding the ATLAS detector response in the presence of multi-lepton signatures. The dataset used corresponds to an integrated luminosity of 1.02 fb−1. The measurement relies on the leptonic decay modes of the W and Z, resulting in final states with electrons, muons, and missing energy. Events are selected by requiring three high momentum leptons, a large missing transverse energy, a Z candidate (reconstructed from two of the leptons) with a mass consistent with the Z pole mass, and a W candidate (reconstructed from the third lepton and the missing energy) with a large transverse mass. The backgrounds to the W±Z process are estimated using Monte Carlo simulations and Data-Driven techniques.
GENERALIZED GEOMETRIC GOPPA CODES

ABSTRACT Conventional geometric Goppa codes are defined in terms of functions of an algebraic function field associated with a divisor evaluated in places of degree 1. The generalization that will be treated here allows evaluations in places of arbitrary degree. With the appropriate inner product, the dual of the code can be defined and described in terms of Weil differentials similarly to conventional geometric Goppa codes. A decoding algorithm is derived.