Miracle-dz/UniFAR-FTUs huggingface dataset:
Watching ion-driven kinetics of ribozyme folding and misfolding caused by energetic and topological frustration one molecule at a time

Folding of ribozymes into well-defined tertiary structures usually requires divalent cations. How Mg2+ ions direct the folding kinetics has been a long-standing unsolved problem because experiments cannot detect the positions and dynamics of ions. To address this problem, we used molecular simulations to dissect the folding kinetics of the Azoarcus ribozyme by monitoring the path each molecule takes to reach the folded state. We quantitatively establish that Mg2+ binding to specific sites, coupled with counter-ion release of monovalent cations, stimulate the formation of secondary and tertiary structures, leading to diverse pathways that include direct rapid folding and trapping in misfolded structures. In some molecules, key tertiary structural elements form when Mg2+ ions bind to specific RNA sites at the earliest stages of the folding, leading to specific collapse and rapid folding. In others, the formation of non-native base pairs, whose rearrangement is needed to reach the folded state, is the rate-limiting step. Escape from energetic traps, driven by thermal fluctuations, occurs readily. In contrast, the transition to the native state from long-lived topologically trapped native-like metastable states is extremely slow. Specific collapse and formation of energetically or topologically frustrated states occur early in the assembly process. Graphical abstract
A model of photosynthetic CO2 assimilation in C3 leaves accounting for respiration and energy recycling by the plastidial oxidative pentose phosphate pathway

- Recently, we reported estimates of anaplerotic carbon flux through the oxidative pentose phosphate pathway (OPPP) in chloroplasts into the Calvin-Benson cycle. These estimates were based on intramolecular hydrogen isotope analysis of sunflower leaf starch. However, the isotope method is believed to underestimate actual flux at low atmospheric CO2 concentration (Ca). - Since the OPPP releases CO2 and reduces NADP+, it can be expected to affect leaf gas exchange under both rubisco- and RuBP-regeneration-limited conditions. Therefore, we expanded Farquhar-von Caemmerer-Berry models to account for OPPP metabolism. Based on model parameterisation with values from the literature, we estimated OPPP-related effects on leaf carbon and energy metabolism in the sunflowers analysed previously. - We found that flux through the plastidial OPPP increases both above and below Ca ≈ 450 ppm (the condition the plants were acclimated to). This is qualitatively consistent with our previous isotope-based estimates, yet gas-exchange-based estimates are larger at low Ca. - We discuss our results in relation to regulatory properties of the plastidial and cytosolic OPPP, the proposed variability of CO2 mesophyll conductance, and the contribution of day respiration to the A/Ci curve drop at high Ca. Furthermore, we critically examine the models and parameterisation and derive recommendations for follow-up studies.
The bandcount increment scenario. III. Deformed structures

Bifurcation structures in two-dimensional parameter spaces formed by chaotic attractors alone are still a long way from being understood completely. In a series of three papers, we investigated the chaotic domain without periodic inclusions for a map, which is considered by many authors as some kind of one-dimensional canonical form for discontinuous maps. In Part I, the basic structures in the chaotic region are explained by the bandcount increment scenario. In Part II, fine self-similar substructures nested into the bandcount increment scenario are explained by the bandcount-adding and -doubling scenarios, nested into each other ad infinitum. Hereby, we fixed in both previous parts one of the parameters to a non-generic value, and studied the remaining two-dimensional parameter subspace. In this Part III, finally we investigated the structures under variation of this third parameter. Remarkably, this step is the most important with respect to practical applications, since it cannot be expected that these operate exactly at the previously investigated specific value.
Gaussian Mixture Modeling Extensions for Improved False Discovery Rate Estimation in GC-MS Metabolomics

The ability to reliably identify small molecules (e.g. metabolites) is key towards driving scientific advancement in metabolomics. Gas chromatography–mass spectrometry (GC-MS) is an analytic method that may be applied to facilitate this process. The typical GC-MS identification workflow involves quantifying the similarity of an observed sample spectrum and other features (e.g. retention index) to that of several references, noting the compound of the best-matching reference spectrum as the identified metabolite. While a deluge of similarity metrics exists, none quantify the error rate of generated identifications, thereby presenting an unknown risk of false identification or discovery. To quantify this unknown risk, we propose a model-based framework for estimating the false discovery rate (FDR) among a set of identifications. Extending a traditional mixture modeling framework, our method incorporates both similarity score and experimental information in estimating the FDR. We apply these models to identification lists derived from across 548 samples of varying complexity and sample type (e.g. fungal species, standard mixtures, etc.), comparing their performance to that of the traditional Gaussian mixture model (GMM). Through simulation, we additionally assess the impact of reference library size on the accuracy of FDR estimates. In comparing the best performing model extensions to the GMM, our results indicate relative decreases in median absolute estimation error (MAE) ranging from 12% to 70%, based on comparisons of the median MAEs across all hit-lists. Results indicate that these relative performance improvements generally hold despite library size, however FDR estimation error typically worsens as the set of reference compounds diminishes. For TOC graphic only
The probabilistic estimation of triplet invariants: the formula P13

The second representation of a triplet invariant [Giacovazzo (1977). Acta Cryst. A33, 933-944] is a collection of special quintets. In the present paper, the triplet is embedded in many more additional quintets obtained in a special way by symmetry operations on the indices of the structure factors. The method of joint probability distribution functions has been used to derive a formula for estimating triplets via the information contained in the basis and in the cross terms of the quintet invariants. The P 10 formula [Cascarano, Giacovazzo, Camalli, Spagna, Burla, Nunzi & Polidori (1984). Acta Cryst. A40, 278-283] is a special case of the new formula, here called P 13 . The new expression has been applied to practical cases
Dynamic Stochastic Programming for Asset-Liability Management

Multistage stochastic programming (in contrast to stochastic control) has found wide application in the formulation and solution of financial problems characterized by a large number of state variables and a generally low number of possible decision stages. The literature on the use of multistage recourse modelling to formalize complex portfolio optimization problems dates back to the early seventies, when the technique was first adopted to solve a fixed interest security portfolio problem. We present here the CALM model which has been designed to deal with uncertainty affecting both assets (in either the portfolio or the market) and liabilities (in the form of scenario dependent payments or borrowing costs). We consider as an instance a pension fund problem in which portfolio rebalancing is allowed over a long-term horizon at discrete time points and where liabilities refer to five different classes of pension contracts. The portfolio manager, given an initial wealth, seeks the maximization of terminal wealth at the horizon, with investment returns modelled as discrete state random vectors. Decision vectors represent possible investments in the market and holding or selling assets in the portfolio, as well as borrowing decisions from a credit line or deposits with a bank. Computational results are presented for a set of 10-stage portfolio problems using different solution methods and libraries (OSL,CPLEX,OB1). The portfolio problem with an underlying vector data process which allows up to 2688 realizations at the 10 year horizon is solved on an IBM RS6000/590 for a set of twenty four large scale test problems using the simplex and barrier methods provided by CPLEX (the latter for either linear or quadratic objective), the predictor/corrector interior point method provided in OB1, the simplex method of OSL, the MSLiP-OSL code instantiating nested Benders decomposition with subproblem solution using OSL simplex and the current version of MSLiP.
Almost sure waiting time results for weak and very weak Bernoulli processes

Asymptotic properties of the waiting time W/sub k/(x, y) until an initial segment of length k of a sample path x of an ergodic finite-alphabet process is seen in an independently chosen sample path y were discussed in earlier papers by Wyner and Ziv (1985), by Noble and Wyner (see IEEE Trans. Inform. Theory, vol.IT-38, p.1551, 1993), and by Shields (see The Journal of Theoretical Probability, vol.6, p.499-519, 1993). These results are sharpened to obtain almost sure convergence in the weak Bernoulli case for exact matches and in the very weak Bernoulli case for approximate matches. The weak Bernoulli proof uses recent results obtained by the authors about estimation of joint distributions, while the very weak Bernoulli result utilizes a new characterization of such processes in terms of a blowing-up property. <<ETX>>
The measure of a matrix as a tool to analyze computer algorithms for circuit analysis

The measure of a matrix is used to, first, bound solutions of ordinary differential equations, bound the computer solution by the backward Euler method, and bound the accumulated truncation error; second, to give conditions for the existence and uniqueness of a dc operating point; third, to determine a convergence region for the Newton-Raphson technique and establish its convergence properties. The unifying idea of the paper is the use of the measure of a matrix.
Local error estimates of the three-dimensional panel methods in terms of the curvilinear surface coordinates

To solve three-dimensional incompressible potential flow problems, panel methods or boundary element methods can be used. These are based on integral equations representing source and dipole distributions over the fluid boundary. The integral equations are expressed in terms of general curvilinear surface coordinates, which serve as coordinates in the computational domain.This paper presents a method of obtaining consistent approximations to the resulting analytical expressions. Estimates of the order of magnitude of the local truncation errors are given. It is shown that, to obtain an $O(\Delta ^3 )$ local truncation error for the potential integrals, a linear source distribution, a quadratic dipole distribution, and a quadratic surface approximation are needed. The same approximations are needed to obtain an $O(\Delta ^2 )$ truncation error in the approximation of the velocity integrals.
PHASE ONE : FROM DIARRHEA IN LOCUSTS TO DYSENTERY

dawn of man’s existence on Earth, and it is only in the past century that an upper hand has been gained in the battle to find consistent methods to combat human and animal disease. This success was seen from two very different fronts at the turn of the 20th century – one biological and one chemical – in the fight to control bacterial diseases such as dysentery, cholera and gangrene. The discovery of bacteriophage has generated little interest for the modern medical community; however, from 1920 to 1940, the practical application and unique properties of bacteriophage to combat many bacterial infections – a practice known as phage therapy – was heralded as a significant advancement in medical care. During this period, antibiotics were also in their developmental stage, and eventually came to be the treatment of choice in western medicine; since that time, there has been an increase in antibiotic resistance around the world, and new approaches to treatment are necessary for communicable disease control (1). For this reason, phage therapy becomes, once again, topical, and a salvo to problems faced by the medical, scientific and environmental health community. Bacteriophage are found wherever bacterial organisms are found; that is, everywhere – in the atmosphere, in the soil, in river water and in the sea, in a direct relationship one to the other. Sewage is an inexhaustible source of all types of bacteriophage, just as it is so for bacteria. The natural reason for this is that bacteriophage are obligatory parasites and can only multiply at the expense of living bacteria; thus, they are found where reproduction is efficient and effective, in those locations where bacteria breed and prosper. Bacteriophage are most abundant in the intestinal contents of all living things that have a digestive tract and can be found in the stools of individuals in a normal state of health. The filtrate from the excreta of individuals that have been passed through Chamberland-type filters will not contain bacteria but only phage; such filtrate on a sensitive culture causes more or less the complete lysis of the microbe (2). Research has demonstrated that under normal conditions, phage are omnipresent in the intestine, and it is estimated that 10 times more phage than bacteria exist in the world. For this reason, it is important to understand their role in the natural cycle and how this role impacts on man. The chronicles of phage therapy will thus be explored in the present report, from the discovery of Felix d’Herelle to the abandonment of its approach, to its reemergence as a potential methodology in active disease control in modern medicine.
Roughness-induced enhancement of giant magnetoresistance in epitaxial Fe/Cr/Fe(001) trilayers

We grow high-quality epitaxial Fe/Cr/Fe trilayers on Au(001) buffer layers and control the roughness of the Fe/Cr interfaces by stopping the deposition of Fe and Cr at a reflection high-energy electron diffraction (RHEED) intensity maximum or minimum. We thus obtain pairs of identical samples which only differ by their interface roughness as confirmed by X-ray reflectivity. Magneto-optical hysteresis loops reveal perfect antiparallel alignment at low fields for all samples. The current-in-plane giant magnetoresistance (CIP-GMR) of trilayers with rougher interfaces is significantly enhanced.
Aggregation of Ice Crystals in Cirrus.

Abstract Results are given from analysis of the aggregation of thick plate, columnar, and bullet rosette ice crystals in cirrus. Data were obtained from PMS 2D-C images, oil coated slides, and aircraft meteorological measurements. Crystal size ranged from 100 to 900 μm in temperatures from −30°C to −45°C. The results indicate that the ratio of the sizes of aggregating crystals and the difference of their terminal velocities are important in aggregation. The collection efficiency was calculated for the thick plate crystals from the same data.
Encodeur hybride pour la détection automatique de désinformation

Résumé L’encodage de texte est aujourd’hui basé sur de larges modèles de langue entièrement neuronaux, utilisés comme des boîtes noires . Afin de répondre au besoin d’explicabilité, nous proposons CATS 1 (Cognitive Attention To Syntax), unecouchepouvantêtreutiliséedanslesréseauxdeneuronesquipermetd’introduireduraisonnementsyntaxiquepourl’encodageetlaclassificationdetextes . Abstract Today, text encoding relies mostly on foundation models, used as black boxes . To bring more transparency, we propose CATS (Cognitive Attention To Syntax), a layer that incorporates syntactic reasoning in neural networks for text classification.
Perdido : librairie Python pour le geoparsing et le geocoding de textes en français

Résumé. Cet article présente la librairie Python Perdido pour le geoparsing et le geocoding de textes en français. Nous présentons l’architecture générale de l’outil Perdido composée de trois couches : back-office, API et librairie Python. Nous détaillons les méthodes utilisées pour le développement de la chaîne de traitement et des différentes tâches (reconnaissance et classification des entités nommées et résolution des toponymes). Enfin, nous présentons les différentes fonctionnalités de la librairie Python et la façon de l’utiliser. La librairie est dé-veloppée comme une surcouche faisant appel aux services de l’API et permet de manipuler, visualiser et exporter les résultats du geoparsing et du geocoding. Un notebook 1 Jupyter décrit, sous la forme d’un tutoriel, l’ensemble des fonction-nalités implémentées dans la librairie.
Astrometric planet searches with SIM PlanetQuest

Abstract SIM will search for planets with masses as small as the Earth's orbiting in the ‘habitable zones’ around more than 100 of the nearest stars and could discover many dozen if Earth-like planets are common. With a planned “Deep Survey” of 100–450 stars (depending on desired mass sensitivity) SIM will search for terrestrial planets around all of the candidate target stars for future direct detection missions such as Terrestrial Planet Finder and Darwin. SIM's “Broad Survey” of 2100 stars will characterize single and multiple-planet systems around a wide variety of stellar types, including many now inaccessible with the radial velocity technique. In particular, SIM will search for planets around young stars providing insights into how planetary systems are born and evolve with time.
P2B-4 Quantitative Analysis of Contrast Enhanced Subharmonic Breast Images

This project was undertaken to demonstrate that quantitative contrast enhanced subharmonic imaging (SHI) can be used to characterize breast lesions in vivo. A modified Logiq 9 scanner (GE Healthcare, Milwaukee, WI) operating in grayscale SHI mode (transmitting/receiving at 4.4/2.2 MHz) was used to study 14 women with 16 breast lesions (4 malignant). Following grayscale and power Doppler imaging (PDI), an ultrasound contrast agent was administrated for PDI and grayscale SHI. Digital clips were acquired and SHI time intensity curves constructed using ImagePro Plus (Media Cybernetics, Silver Spring, MD). SHI perfusion estimates were determined using a linear relationship based on the slope of the initial SHI uptake (previously established in a canine model). Perfusion was determined within 3 regions of interest, (ROIs) encompassing the centre, the periphery or the entire lesion. Cumulative Maximum Intensity (CMI) images were constructed from SHI through maximum intensity capture of temporal data in consecutive images to better visualize tumor neovascularity. The mean transit time was calculated for each lesion. The degree of vascularity observed with PDI and with contrast-enhanced PDI both correlated with SHI (r 2 ≥0.40; p 0.32). CMI imaging provided a better depiction of the tortuous angiogenic vascular morphology associated with breast lesions. The mean transit time was lower in malignant than in benign masses (0.72s±0.19s vs. 1.31s±0.72s; p= 0.02). In conclusion, quantitative methods for analyzing in vivo grayscale SHI have been tested in breast lesions. Preliminary results indicate that perfusion and mean transit time may improve the characterization of malignant and benign breast masses. However, the current patient population is very small and further studies are required to substantiate these findings.
UAV multispectral multi-domain feature optimization for the air-to-ground recognition of outdoor injured human targets under cross-scene environment

Objective UAV-based multispectral detection and identification technology for ground injured human targets, is a novel and promising unmanned technology for public health and safety IoT applications, such as outdoor lost injured searching and battlefield casualty searching, and our previous research has demonstrated its feasibility. However, in practical applications, the searched human target always exhibits low target-background contrast relative to the vast and diverse surrounding environment, and the ground environment also shifts randomly during the UAV cruise process. These two key factors make it difficult to achieve highly robust, stable, and accurate recognition performance under the cross-scene situation. Methods This paper proposes a cross-scene multi-domain feature joint optimization (CMFJO) for cross-scene outdoor static human target recognition. Results In the experiments, we first investigated the impact severity of the cross-scene problem and the necessity to solve it by designing 3 typical single-scene experiments. Experimental results show that although a single-scene model holds good recognition capability for its scenes (96.35% in desert scenes, 99.81% in woodland scenes, and 97.39% in urban scenes), its recognition performance for other scenes deteriorates sharply (below 75% overall) after scene changes. On the other hand, the proposed CMFJO method was also validated using the same cross-scene feature dataset. The recognition results for both individual scene and composite scene show that this method could achieve an average classification accuracy of 92.55% under cross-scene situation. Discussion This study first tried to construct an excellent cross-scene recognition model for the human target recognition, named CMFJO method, which is based on multispectral multi-domain feature vectors with scenario-independent, stable and efficient target recognition capability. It will significantly improve the accuracy and usability of UAV-based multispectral technology method for outdoor injured human target search in practical applications and provide a powerful supporting technology for public safety and health.
Regeneration of the dermal skeleton and wound epidermis formation depend on BMP signaling in the caudal fin of platyfish

Fin regeneration has been extensively studied in zebrafish, a genetic model organism. Little is known about regulators of this process in distant fish taxa, such as the Poeciliidae family, represented by the platyfish. Here, we used this species to investigate the plasticity of ray branching morphogenesis following either straight amputation or excision of ray triplets. This approach revealed that ray branching can be conditionally shifted to a more distal position, suggesting non-autonomous regulation of bone patterning. To gain molecular insights into regeneration of fin-specific dermal skeleton elements, actinotrichia and lepidotrichia, we localized expression of the actinodin genes and bmp2 in the regenerative outgrowth. Blocking of the BMP type-I receptor suppressed phospho-Smad1/5 immunoreactivity, and impaired fin regeneration after blastema formation. The resulting phenotype was characterized by the absence of bone and actinotrichia restoration. In addition, the wound epidermis displayed extensive thickening. This malformation was associated with expanded Tp63 expression from the basal epithelium towards more superficial layers, suggesting abnormal tissue differentiation. Our data add to the increasing evidence for the integrative role of BMP signaling in epidermal and skeletal tissue formation during fin regeneration. This expands our understanding of common mechanisms guiding appendage restoration in diverse clades of teleosts.