Miracle-dz/UniFAR-FTUs huggingface dataset:
Histone variants shape chromatin states in Arabidopsis

How different intrinsic sequence variation or regulatory modifications of histones regulate nucleosome interactions with transcription remain unclear. By contrast with H3 and H2B variants, H2A variants occupy specific domains of chromatin in Arabidopsis thaliana. Broad domains of chromatin are affected by the loss of remodelers that affect the deposition or the exchange of H2A variants. Notably, the chromatin remodeler DECREASED IN DNA METHYLATION (DDM1) is required to maintain enrichment in all markers of constitutive heterochromatin including DNA methylation, H3K9me1/2 and the variant H2A.W. To test the importance of histone variants in the organization of chromatin we investigated how histone variants and histone modifications assemble in the Arabidopsis thaliana genome and showed that a limited number of chromatin states divide euchromatin and heterochromatin into several subdomains. We found that histone variants are as significant as histone modifications in determining the composition of chromatin states. Particularly strong associations were observed between H2A variants and specific combinations of histone modifications. To study the role of H2A variants in organizing chromatin states we determined the role the chromatin remodeler DECREASED IN DNA METHYLATION (DDM1) in the organization of chromatin states. We showed that the loss of DDM1 prevented the exchange of the histone variant H2A.Z to H2A.W in constitutive heterochromatin, resulting in significant effects on the definition and distribution of chromatin states in and outside of heterochromatin. We thus propose that dynamic exchanges of histone variants control the organization of histone modifications into chromatin states, acting as molecular landmarks.
Teaching mathematics to deaf children

Preface.Acknowledgements. Conventions used for descriptions of interviews.Chapter 1 Introduction.Chapter 2 Counting and its creative uses.Chapter 3 Additive reasoning: connecting addition and subtraction.Chapter 4 Reading and writing numbers.Chapter 5 Multiplicative reasoning: connecting multiplication, division and many other mathematical ideas.Chapter 6 Teaching mathematics to deaf children: how the story began and the happy ending.References. Index.
Scaling of Protein Function across the Tree of Life

Scaling laws are a powerful way to compare genomes because they put all organisms onto a single curve and reveal non-trivial generalities as genomes change in size. The abundance of functional categories in a given genome scales with genome size, suggesting that universal constraints shape category abundance. Here we look across the tree of life to understand how genome evolution may be related to functional scaling. We revisit previous observations of functional genome scaling with an expanded taxonomy by analyzing 3726 bacterial, 220 archaeal, and 79 unicellular eukaryotic genomes. We find that for some functional classes, scaling is best described by multiple exponents, revealing previously unobserved shifts in scaling as genomes grow or contract. Furthermore, scaling varies between phyletic groups and is less universal than previously thought, with scaling shifts varying uniquely between domains and scaling exponents varying uniquely between phyla. We also find that individual phyla frequently span scaling exponents of functional classes, revealing that individual clades can move across scaling exponents. Across the tree of life, variability in functional scaling is not accounted for by genome phylogeny, suggesting that physiological and/or cell plan outweighs phylogeny.
Visualizing proteins by expansion microscopy

Fluorescence imaging is one of the most versatile and widely-used tools in biology1. Although techniques to overcome the diffraction barrier were introduced more than two decades ago, and the nominal attainable resolution kept improving2, 3, fluorescence microscopy still fails to image the morphology of single proteins or small molecular complexes, either purified or in a cellular context4, 5. Here we report a solution to this problem, in the form of one-step nanoscale expansion (ONE) microscopy. We combined the 10-fold axial expansion of the specimen (1000-fold by volume) with a fluorescence fluctuation analysis6, 7 to enable the description of cultured cells, tissues, viral particles, molecular complexes and single proteins. At the cellular level, using immunostaining, our technology revealed detailed nanoscale arrangements of synaptic proteins, including a quasi-regular organisation of PSD95 clusters. At the single molecule level, upon main chain fluorescent labelling, we could visualise the shape of individual membrane and soluble proteins. Moreover, conformational changes undergone by the ∼17 kDa protein calmodulin upon Ca2+ binding were readily observable. We also imaged and classified molecular aggregates in cerebrospinal fluid samples from Parkinson’s Disease (PD) patients, which represents a promising new development towards improved PD diagnosis. ONE microscopy is compatible with conventional microscopes and can be performed with the software we provide here as a free, open-source package. This technology bridges the gap between high-resolution structural biology techniques and light microscopy, and provides a new avenue for discoveries in biology and medicine.
A weak degeneracy revealing decomposition for the CANDECOMP/PARAFAC model

The CANDECOMP/PARAFAC (CP) model is a well known and frequently used tool for extracting substantial information from a three‐way data array. It has several useful characteristics and usually gives meaningful insights about the underlying structure of the data. However, in some cases it has a ‘strange’ behaviour suffering from the so‐called ‘degenerate solutions’, i.e. solutions where the components show a diverging pattern and are meaningless. Several authors have investigated the causes of degeneracy concluding that the phenomenon is due to a lack of minimum of the loss function. In this paper, we study the degeneracy of CP limiting our attention to the two‐component case. The study is done by introducing a canonical form, called 2DR, which is ‘weakly degeneracy revealing’. On the ground of this framework, degeneracy is studied along with some of the remedies proposed in the literature by using a Tucker3 model having a core in the 2DR form. The analysis gives new insights about the behaviour of the CP model and suggests new ideas on how to deal with degeneracy. Copyright © 2010 John Wiley & Sons, Ltd.
Overcoming Label Noise for Source-free Unsupervised Video Domain Adaptation

Despite the progress seen in classification methods, current approaches for handling videos with distribution shifts in source and target domains remain source-dependent as they require access to the source data during the adaptation stage. In this paper, we present a self-training based source-free video domain adaptation approach (without bells and whistles) to address this challenge by bridging the gap between the source and the target domains. We use the source pre-trained model to generate pseudo-labels for the target domain samples, which are inevitably noisy. We treat the problem of source-free video domain adaptation as learning from noisy labels and argue that the samples with correct pseudo-labels can help in the adaptation stage. To this end, we leverage the cross-entropy loss as an indicator of the correctness of pseudo-labels, and use the resulting small-loss samples from the target domain for fine-tuning the model. Extensive experimental evaluations show that our method termed as CleanAdapt achieves gain over the source-only model and outperforms the state-of-the-art approaches on various open datasets.
Stability of body‐centered polygonal configurations of ideal vortices

Thomson’s results concerning the stability of regular vortex polygons are generalized to include the case of the polygonal center being occupied by a vortex of arbitrary relative strength. Of most significance is the fact that a strong enough central vortex can stabilize a Thomson polygon consisting of arbitrarily many vortices. The efficacy of the free energy criterion for stability is demonstrated in showing that the Thomson heptagon is stable.
An instrument for the high temperature measurement of the Seebeck coefficient and electrical resistivity

A system for the simultaneous measurement of thermoelectric power and resistivity of one and/or two samples over a temperature range of 300–1000 K in a vacuum chamber is designed and implemented. A sample probe is developed to provide its easy mounting and usage. In addition, two samples can be measured at the same time. Measurement accuracy has been enhanced by beadless thermocouples and micro-heaters that are specifically designed in order to minimize the ‘cold-finger effect’ and to eliminate some possible source of contact, design and measurement errors. A broad range of physical types and shapes of samples, such as bulk, bar or disc, can be measured by a software controlled system. A differential steady-state method has been applied for Seebeck coefficient measurement. Resistivity measurement is conducted with the axial technique of the four-point probe method. Platinum wire and a niobium rod are chosen as the standard samples. The total data error for the Seebeck coefficient and resistivity measurements is estimated to be less than 2.6% and 1%, respectively.
Full-Scale Turbine Vane Endwall Film-Cooling Effectiveness Distribution Using Pressure-Sensitive Paint Technique

Researchers in gas turbine field take great interest in the cooling performance on the first-stage vane because of the complex flow characteristics and intensive heat load that comes from the exit of the combustion chamber. A better understanding is needed on how the coolant flow interacts with the mainstream and the resulting cooling effect in the real engine especially for the first-stage vane. An authentic flow channel and condition should be achieved. In this study, three full-scale turbine vanes are used to construct an annular-sector cascade. The film-cooling design is attained through numerous layback fan-shaped and cylindrical holes dispersed on the vane and both endwalls. With the three-dimensional vane geometry and corresponding wind tunnel design, the true flow field can thus be simulated as in the engine. This study targets the film-cooling effectiveness on the inner endwall (hub) of turbine vane. Tests are performed under the mainstream Reynolds number 350,000; the related inlet Mach number is 0.09; and the freestream turbulence intensity is 8%. Two variables, coolant-to-mainstream mass flow ratios (MFR = 2%, 3%, and 4%) and density ratios (DR = 1.0 and 1.5), are examined. Pressure-sensitive paint (PSP) technique is utilized to capture the detail contour of film-cooling effectiveness on the inner endwall and demonstrate the coolant trace. The presented results serve as a comparison basis for other sets of vanes with different cooling designs. The results are expected to strengthen the promise of PSP technique on evaluating the film-cooling performance of the engine geometries.
What is a Good Information Proxy?

This article compares the qualities of several intraday activity measures as information proxy. These information proxies are: - the number of trades; - the volume of trades, - the number of incoming orders; - the volume of incomings orders. Relying on the MDH hypothesis, a good information proxy should induce a reduction of the well known deviations from the Markov-Gaussian hypothesis. Although, this approach has rarely been used at an intraday level. This articles uses several time deformations: the time is not measured in number of minutes and seconds but according to a measure of the activity. All the time deformations respect the daily structure of the data: we only distort the time measurement between the first and the last trade on each day. We then analyze the returns properties in these time measurements. The distance between the empirical facts we observe and the theoretical properties we expect enables us to rank the activity measures. Two different ways are used to compare the activity measures. First, we evaluate the reduction of the well known intraday patterns. Second, we compare the statistical properties of the returns. The conclusion of these two criteria are broadly consistent: None of the activity measure satisfy the validation criteria (disappearance of the intraday pattern and normality of the returns). Although, this study leads to several interesting conclusions. First, activity measures from the trades are better than from those from the incomings orders. Second, a number of events is preferable to a volume of events. Hence, the ranking among the four activity measures is: the number of trades, the volume of trades, the number of orders introduced, the volume of orders. This study also underlines that the results are influenced by the interval length. For instance, according to the length, the volume may or may not have an information content beyond the number of trades. This fact suggests that a better understanding of the micro-phenomena (trade-by-trade study) is required to get a firm conclusion about the informational relationships at an intraday level.
Some axially symmetric potential problems

Abstract Some axially symmetric boundary value problems of potential theory are formulated as integral equations of the first kind. In each case the kernel admits an expansion, for small values of a parameter of the problem, that leads to an approximate integral equation whose solution provides a direct asymptotic estimate for the physical quantity of primary interest. A manipulation of the original and modified integral equations provides an efficient formula for calculating higher order terms in the asymptotic expansion.
Susceptible‐infected‐recovered models with natural birth and death on complex networks

This paper proposes two modified susceptible‐infected‐recovered (SIRS) models on homogenous and heterogeneous networks, respectively. In the study of the homogenous network model, Lyapunov functions are used to study the globally asymptotically stable of the equilibria of the model. It is proved that if the basic reproduction number of the model is less than one, then the disease‐free equilibrium is globally asymptotically stable, otherwise, the endemic equilibrium is globally asymptotically stable. In the study of the heterogeneous network model, the existences of the disease‐free equilibrium and epidemic equilibrium of the model are discussed. A threshold value R˜0 is given. It is proved that if the threshold value R˜0 of the model is less than one, then the disease‐free equilibrium is globally asymptotically stable. The simulation examples on the two SIRS models are given. Copyright © 2013 John Wiley & Sons, Ltd.
The Upper Limit of "Musical" Pitch

Ten musicians were presented with a transposable melodic sequence of two monaural pure tones and were required to set the pitch of the higher tone in the sequence just above the upper limit of "musical" pitch. The overall mean of the frequency adjustments was 4.7 kHz, but subjects9 individual means consistently differed from each other; their standard deviation was about three semitones. Subjects9 adjustments depended on the range of possible adjustments and thus were influenced by context factors. However, the effect of range was 2.7 times smaller than it should have been if the upper limit of musical pitch had no perceptual reality. No consistent frequency differences were found between adjustments made for tones heard through the left ear and the right ear. However, in an additional study on six nonmusicians, one subject displayed a systematic interaural frequency difference amounting to about one semitone. Control measurements showed that this difference could not be explained by the subject9s binaural diplacusis. Thus, as suggested by Bachem in 1937, it seems that the upper limit of musical pitch can be a different pitch for the two ears of the same subject.
Resonance production in the π\(^+\) π\(^-\) decay channel in proton - proton collisions at 7 TeV

Short lived resonances can be used as a useful probe into the fundamental interactions that occur within the collisions of particles at high energy, as conducted in high energy experiments, such as the ones performed at the A Large Ion Collider Experiment (ALICE) experiment at the Large Hadron Collider (LHC). The environments studied range from the broad hadronic interactions created within the collisions of protons at unexplored centre-of-mass energies, to an entirely different form of hadronic matter created in the hot and dense region resulting from colliding heavy ions at high energy. However, due to the short lifetimes of resonances, they cannot be measured directly and instead must be studied using the products they decay into. The analysis conducted focuses on the extraction of a number of resonances seen in the π\(^+\) π\(^-\) channel; the invariant mass spectrum created contains many components which need to be accounted for within the extraction process, which also requires numerous corrections applied to it in order to accurately measure the desired peaks.
Validity of Forchheimer Equation in Radial Flow through Coarse Granular Media

The validity of application of the Forchheimer equation for steady non-Darcy radial flow through coarse granular media and glass spheres has been investigated experimentally. The drawbacks observed while computing the coefficients of this equation have been critically reviewed. An expression is obtained for hydraulic gradient in the case of radial flow. For coarse granular media, a relationship between specific surface and volume diameter has been obtained. In the range of experiments conducted lying in turbulent regime (300 < R < 7,000) a simple form of expression absorbing the effects of variations in size of the medium, number of sizes of the samples used, and porosity of the medium relating resistance to flow and flow pattern in a converging flow configuration is developed. Porosity effect and wall effect are included to make the results of the study more realistic and practically applicable.
Optical interaction between small plasmonic nanowires: a perspective from induced forces and torques

This paper addresses a new numerical study of the near electromagnetic coupling between two small, metallic nanowires under plane-wave illumination. The forces and torques induced give a different point of view of the interaction. The analysis of these near-field, mechanical observables is based entirely on the plasmon hybridization model, with the help of an adequate correlation with far fields. Although several studies of the opto-mechanical inductions have been done, unexpected features of the movement are obtained. ‘Coordinated’ spin for the wires are found, in addition to binding or repulsion forces between the wires and scattering forces. For heterodimers, also orbital torques are obtained. The binding and rotation of the nanowires as well as orbital torques are strongly dependent on the plasmonic excitations of the system. They identify uniquely the surface plasmons. In particular, dark modes can be optically detected without using evanescent fields. The optical forces and torques are calculated exactly by Maxwell stress tensor. ‘Realistic’ infinite nanowires of silver and gold are simulated by a size correction in bulk dielectric function. Thus, the importance of this correction on the mechanical results is also studied. The results can contribute to the design of devices for real observation/detection of surface plasmons. The spectra of forces, and specially of torques, show more resolved resonances because overlapping effects are not as present as in far-field calculations. The spinning of wires found and the analysis made could open new directions of studies and applications of dimers.
Numerical study of gas–solid drag models in a bubbling fluidized bed

ABSTRACT Bubbling fluidized beds find application mainly in power conversion industries. For design, dimensioning, and operation of fluidized bed equipment, the understanding of multiphase gas–solid flows is of great importance. The use of computational fluid dynamics in the simulation of gas–solid systems is limited by the complexity of mathematical models, which rely on a series of empirical or theoretical correlations. In the present work, the code Multiphase Flow with Interphase eXchanges (MFIX) was employed to simulate flows in a bubbling fluidized bed and to compare results predicted using different gas–solid drag models. A two-fluid model with kinetic theory of granular flows (TFM-KTGF) was employed, in which gas–solid drag correlations, such as Gidaspow, Hill-Koch-Ladd, or Syamlal and O’Brien, were applied to model momentum transfer between phases. The results predicted were compared with each other and with experimental results from the literature. It was found that the results predicted using each model differ much. The Gidaspow and Hill-Koch-Ladd models yielded bubbles with shapes more similar to the experiments.
Isolation and characterization of polyhydroxyalkanoate (PHA) producing bacteria isolate from landfill land of Kampung Jawa Banda Aceh

The production of biodegradable plastic from microorganisms has great potential as a substitute for conventional plastic. This study aims to isolate bacterial strains capable of polyhydroxyalkanoates (PHAs) production from the Kampung Jawa landfill land (KJLL) and characterize biopolymers. The bacterial strains were able to produce PHA using a mineral salt medium (MSM) with glucose as a carbon source. The qualitative screening of PHA-producing bacteria was conducted by Sudan Black and Nile Red. Of the 64 bacteria strains, only 41 were able to accumulate PHA in Sudan Black and Nile Red. The results showed that one bacteria the Coccobacillus strain had the highest color intensity for further characterization of PHA. The characterization of PHA by Differential Scanning Calorimetry (DSC) and Thermogravimetric Analysis (TGA) showed a melting temperature (Tm) of 101.54°C. X-ray diffraction (XRD) analysis revealed a crystalline structure with an index crystallinity (ICr) value of 15.82% for PHA. The results of the analysis proved that PHA was produced by bacteria isolate. This study suggests that this is the first report of the bacteria from the Kampung Jawa landfill producing PHA with good characteristics and potential biotechnology applications.
ChargePrint: A Framework for Internet-Scale Discovery and Security Analysis of EV Charging Management Systems

—Electric Vehicle Charging Management Systems (EVCMS) are a collection of specialized software that allow users to remotely operate Electric Vehicle Charging Stations (EVCS). With the increasing number of deployed EVCS to support the growing global EV fleet, the number of EVCMS are consequently growing, which introduces a new attack surface. In this paper, we propose a novel multi-stage framework, ChargePrint, to discover Internet-connected EVCMS and investigate their security posture. ChargePrint leverages identifiers extracted from a small seed of EVCMS to extend the capabilities of device search engines through iterative fingerprinting and a combination of classification and clustering approaches. Using initial seeds from 1,800 discovered hosts that deployed 9 distinct EVCMS, we identified 27,439 online EVCS instrumented by 44 unique EVCMS. Consequently, our in-depth security analysis highlights the insecurity of the deployed EVCMS by uncovering 120 0-day vulnerabilities, which shed light on the feasibility of cyber attacks against the EVCS, its users, and the connected power grid. Finally, while we recommend countermeasures to mitigate future threats, we contribute to the security of the EVCS ecosystem by conducting a Coordinated Vulnerability Disclosure (CVD) effort with system developers/vendors who acknowledged and assigned the discovered vulnerabilities more than 20 CVE-IDs.