Miracle-dz/UniFAR-FTUs huggingface dataset:
The timing of transcription of RpoS-dependent genes varies across multiple stresses in Escherichia coli K-12

ABSTRACT The alternative sigma factor RpoS regulates transcription of over 1,000 genes in Escherichia coli in response to many different stresses. RpoS levels rise continuously after exposure to stress, and the consequences of changing levels of RpoS for the temporal patterns of expression of RpoS-regulated genes have not been described. We measured RpoS levels at various times during the entry to stationary phase, or in response to high osmolarity or low temperature, and found that the time required to reach maximum levels varied by several hours. We quantified the transcriptome across these stresses using RNA-seq. The number of differentially expressed genes differed among stresses, with 1,379 DE genes identified in stationary phase, 633 in high osmolarity, and 302 in cold shock. To quantify the timing of gene expression, we fit sigmoid or double sigmoid models to differentially expressed genes in each stress. During the entry into stationary phase, genes whose expression rose earlier tended to be those that had been found to respond most strongly to low levels of RpoS. The timing of individual gene’s expression was not correlated across stresses. Taken together, our results demonstrate E. coli activates RpoS with different timing in response to different stresses, which in turn generates a unique pattern of timing of the transcription response to each stress. IMPORTANCE Bacteria adapt to changing environments by altering the transcription of their genes. Specific proteins can regulate these changes. This study explored how a single protein called RpoS controls how many genes change expression during adaptation to three stresses. We found that: (i) RpoS is responsible for activating different genes in different stresses; (ii) that during a stress, the timing of gene activation depends on the what stress it is; and (iii) that how much RpoS a gene needs in order to be activated can predict when that gene will be activated during the stress of stationary phase. Bacteria adapt to changing environments by altering the transcription of their genes. Specific proteins can regulate these changes. This study explored how a single protein called RpoS controls how many genes change expression during adaptation to three stresses. We found that: (i) RpoS is responsible for activating different genes in different stresses; (ii) that during a stress, the timing of gene activation depends on the what stress it is; and (iii) that how much RpoS a gene needs in order to be activated can predict when that gene will be activated during the stress of stationary phase.
Evolution of horn length and lifting strength in the Japanese rhinoceros beetle Trypoxylus dichotomus


Rhinoceros beetle (Trypoxylus dichotomus) males have pitchfork-shaped head horns, which they use to pry rival males from the trunks of trees. In the largest males these horns can be three times the length of horns in the two closest sister species. Because this weapon functions as a lever, longer horns should lift with less force than shorter horns (the ‘paradox of the weakening combatant’) unless other elements of the weapon system (e.g., input lever length, muscle mass) evolve to compensate. We used next-generation sequencing approaches to consolidate 23 sample locations into 8 genetically distinguishable populations, reconstructing their historical relationships and providing a comprehensive picture of the evolution of this horn lever system. We show that head horns likely increased in length independently in the Northern and Southern lineages. In both instances this resulted in weaker lifting forces, but this mechanical disadvantage was later ameliorated, to some extent and in some locations, by subsequent reductions to horn length, changes in muscle size, or by an increase in input lever length (head height). Our results reveal an exciting geographic mosaic of differences in weapon size, weapon force, and in the extent and nature of mechanical compensation. Reconstructing the evolution of this weapon system offers critical insights towards meaningfully linking mating system dynamics, selection patterns, and diversity in sexually selected traits.
Concerning the Problem of Subsets of Finite Positive Packing Measure

For every Hausdorff function h, the paper gives a construction of a compact metric space of infinite diameter‐based h‐packing measure which has no subsets of positive finite measure. It then indicates how such a construction can be modified to provide the same result for a radius‐based packing measure in the case of certain Hausdorff functions which do not satisfy a doubling condition. This is in surprising contrast to another result which shows that for a particular radius‐based definition of packing measure no such example can be found.
Cotranscriptional demethylation induces global loss of H3K4me2 from active genes in Arabidopsis

Based on studies of animals and yeasts, methylation of histone H3 lysine 4 (H3K4me1/2/3, for mono-, di-, and tri-methylation, respectively) is regarded as the key epigenetic modification of transcriptionally active genes. In plants, however, H3K4me2 correlates negatively with transcription, and the regulatory mechanisms of this counterintuitive H3K4me2 distribution in plants remain largely unexplored. A previous genetic screen for factors regulating plant regeneration identified Arabidopsis LYSINE-SPECIFIC DEMETHYLASE 1-LIKE 3 (LDL3), which is a major H3K4me2 demethylase. Here, we show that LDL3-mediated H3K4me2 demethylation depends on the transcription elongation factor Paf1C and phosphorylation of the C-terminal domain (CTD) of RNA polymerase II (RNAPII). In addition, LDL3 binds to phosphorylated RNAPII. These results suggest that LDL3 is recruited to transcribed genes by binding to elongating RNAPII and demethylates H3K4me2 cotranscriptionally. Importantly, the negative correlation between H3K4me2 and transcription is disrupted in the ldl3 mutant, demonstrating the genome-wide impacts of the transcription-driven LDL3 pathway to control H3K4me2 in plants. Our findings implicate H3K4me2 in plants as chromatin memory for transcriptionally repressive states, which ensures robust gene control.
Nanojunctions: Specificity of Ca2+ signalling requires nano-scale architecture of intracellular membrane contact sites

Specificity of control over virtually all essential cellular functions by Ca2+ is based on the existence of separated, autonomic signaling modules. Spatiotemporal definition of Ca2+ signals involves the assembly of signaling complexes within the nano-architecture of contact sites between the sarco/endoplasmic (SR/ER) reticulum and the plasma membrane (PM). While the requirement of precise spatial assembly and positioning of the junctional signaling elements is well documented, the role of the nano-scale membrane architecture itself, as an ion reflecting confinement of the signaling unit, remains as yet elusive. Utilizing the NCX1/SERCA2-mediated ER Ca2+ refilling process as a junctional signalling paradigm, we provide here the first evidence for an indispensable cellular function of the junctional membrane architecture. Our stochastic modeling approach demonstrates that junctional ER Ca2+refilling operates exclusively at nano-scale membrane spacing, with a strong inverse relationship between junctional width and signaling efficiency. Our model predicts a breakdown of junctional Ca2+ signaling with loss of reflecting membrane confinement, irrespective of the spatial positioning of the molecular signaling elements. Alterations in the molecular and nano-scale membrane organization at organelle-PM contacts are suggested as new concept in pathophysiology.
An Ensemble Cumulus Convection Parameterization with Explicit Cloud Treatment

Abstract The paper describes a convection parameterization employing a new formulation of the quasi-equilibrium closure hypothesis of Arakawa and Schubert. The scheme models a full spectrum of different cumulus clouds and its evolution within one time step of the host global climate model. Each cloud is simulated using a one-dimensional Lagrangian entraining parcel model, which includes mixed phase microphysics and vertical velocity. Hence, the model delivers explicit information on distribution of vertical velocities, precipitation intensities, cloud heights, and cloud coverage. The parameterization is evaluated in the ECHAM single-column model for midlatitude summer and tropical convection. Results show an improved temporal distribution, including the diurnal cycle, of convective heating and moistening in comparison to the Tiedtke–Nordeng scheme, which is the standard convection parameterization within ECHAM. The amount and temporal distribution of precipitation are clearly improved compared with the or.
BEAM: a combinatorial recombinase toolbox for binary gene expression and mosaic analysis

Genetic mosaic analysis, in which mutant cells reside intermingled with wild-type cells, is a powerful experimental approach, but has not been widely used in mice because existing genome-based strategies require complicated and protracted breeding schemes. We have developed an alternative approach termed BEAM (for Binary Expression Aleatory Mosaic) that relies on sparse recombinase activation to generate two genetically distinct, non-overlapping populations of cells for comparative analysis. Following delivery of DNA constructs by transfection or viral transduction, combinatorial recombinase activity generates two distinct populations of cells labeled with either green or red fluorescent protein. Any gene of interest can be mis-expressed or deleted in one population for comparison with intermingled control cells. We have extensively optimized and characterized this system both in vitro and in vivo, and demonstrate its power for investigating cell autonomy, identifying temporally or spatially aberrant phenotypes, revealing changes in cell proliferation or death, and controlling for procedural variability.
Ray trajectories in an absorptive ionosphere

Simulates EM ray propagation in a cold collisional ionosphere in the presence of the geomagnetic field. A novel aspect is our attempt to assess the effect of absorption on the ray trajectories, not merely the field intensity. The present model is based on the familiar Appelton-Hartree dispersion equation for the cold, collisional, magnetized ionosphere, where slow variation (on the scale of a wavelength) of the terrestrial magnetic field is assumed. Unlike some studies which first compute the lossless trajectories, and then add on a posteriori the attenuation along these trajectories, as a perturbation of the lossless solution, here the Hamiltonian ray tracing formalism is extended in order to include the absorption effects in the formalism a priori. High losses are considered in order to emphasize the effects. The present study contributes to our understanding of the basic problem of ray propagation in the presence of arbitrary losses. The variation of the ray paths with frequency, launching angle, collision frequency, electron density profile and other variables, are examined for the Chapman type F layer. Results for various conditions are displayed. By using typical F layer parameters, it is found that, in certain cases, high collision frequency affects the ray path by as much as 500 km. The paper is motivated by over-the-horizon radar.
AC loss characteristics of Bi2223 twisted multifilamentary tape in AC longitudinal magnetic field

AC loss characteristics of the twisted multifilamentary high temperature superconducting tape with different twist pitches in external AC longitudinal magnetic field as well as those of the nontwisted tape were experimentally investigated. We measured the AC transport current loss and the AC magnetization loss in the twisted and nontwisted Bi2223 multifilamentary tapes in the external AC longitudinal magnetic field. The measured transport loss and magnetization loss in the twisted tapes were affected by the amplitude and the direction of the AC longitudinal field. It was also shown that the AC losses in the tapes under the external AC longitudinal field depended on the twist pitch.
Mismatch between human early visual cortex and perception in spatial extent representation: Radial bias shapes cortical representation while co-axial bias shapes perception

An object occupies an enclosed region in the visual field, which defines its spatial extent. Humans display exquisite finesse in spatial extent perception. Recent series of human neuroimaging and monkey single-cell studies suggest the spatial representation encoded in the early visual cortex (EVC) as the neural substrate of spatial extent estimation. Guided by this “EVC hypothesis” on spatial extent estimation, we predicted that human estimation of spatial extents would reflect the topographic biases known to exist in EVC’s spatial representation, the co-axial and radial biases. To test this prediction, we concurrently assessed those two spatial biases in both EVC’s and perceptual spatial representations by probing the anisotropy of EVC’s population receptive fields, on the one hand, and that of humans’ spatial extent estimation, on the other hand. To our surprise, we found a marked topographic mismatch between EVC’s and perceptual representations of oriented visual patterns, the radial bias in the former and the co-axial bias in the latter. Amid this topographic mismatch, the extent to which the anisotropy of spatial extents is modulated by stimulus orientation is correlated across individuals between EVC and perception. Our findings seem to require a revision of the current understanding of EVC’s functional architecture and contribution to visual perception: EVC’s spatial representation (i) is governed by the radial bias but only weakly modulated by the co-axial bias, and (ii) do contribute to spatial extent perception, but in a limited way where additional neural mechanisms are called in to counteract the radial bias in EVC. Significant statement Previous anatomical and functional studies suggest both radial and co-axial biases as topographic factors governing the spatial representation of the early visual cortex (EVC). On the other hand, EVC’s fine-grained spatial representation has been considered the most plausible neural substrate for exquisite human perception of spatial extents. Based on these suggestions, we reasoned that these two topographic biases are likely to be shared between EVC’s and perceptual representations of spatial extents. However, our neuroimaging and psychophysics experiments implicate a need for revising those two suggestions. Firstly, the co-axial bias seems to exert only a modulatory influence on EVC’s functional architecture. Secondly, human spatial extent perception requires further contribution from neural mechanisms that correct EVC’s spatial representation for its radial bias.
Genetic Screen Uncovers a Dual Role for Phospholipids in Mitochondrial-Derived Compartment Biogenesis

Cells utilize multiple mechanisms to maintain mitochondrial homeostasis in response to stress. We recently identified a cellular structure, called the mitochondria-derived compartment (MDC), that is generated from mitochondria in response to amino acid overabundance. MDCs selectively sequester proteins from mitochondria for subsequent degradation, and loss of MDCs sensitizes cells to amino acid stress. Here, we conducted a microscopy-based screen in budding yeast to identify factors that regulate MDC formation. We found that levels of two mitochondrial phospholipids, cardiolipin (CL) and phosphatidylethanolamine (PE), regulate MDC biogenesis in opposing directions. CL depletion impairs MDC biogenesis, whereas PE reduction leads to constitutive MDC formation. Additionally, in response to MDC-inducing agents, cellular and mitochondrial PE declines in an amino acid-dependent manner. Overexpressing mitochondrial PE synthesis pathway components suppresses MDC biogenesis during amino acid stress. Altogether, our data indicate a requirement for CL in MDC biogenesis, and suggest that PE depletion may serve as a regulatory signal for MDC formation downstream of MDC-inducing metabolic stress. SUMMARY Xiao et al. identify distinct roles for the phospholipids cardiolipin and phosphatidylethanolamine in mitochondria-derived compartment (MDC) biogenesis. They show that cardiolipin is required for MDC formation, whereas a decline in phosphatidylethanolamine in response to amino acid stress triggers MDC biogenesis.
Proliferating cell nuclear antigen involves in temperature stress tolerance of Ulva prolifera

Ulva prolifera is the dominant species of “green tide”, and has higher tolerance to environmental stresses such as temperature. However, the molecular mechanisms are still unclear. Here, transcriptome analysis, Western blot and RT-qPCR analysis of U. prolifera suggested that, under temperature stresses (4°C, 36°C), the expression of PCNA and CyclinA was promoted, and the MAPK signaling was activated. Besides, the results showed that PCNA interacted with CyclinA. Interestingly, the expression of miR-2916, which was predicted to bind PCNA at -552∼-772, was negatively correlated with the expression of PCNA under temperature stresses (4°C, 36°C). In addition, the results showed that low temperature (4°C) had no obvious effect on the survival, the formation of cell walls, and the division of protoplasts. However, high temperature (36°C) had obvious effect on them. PCNA inhibitors increased the sensitivity of the protoplasts under temperature stresses. Together, our results suggested PCNA regulating the proliferation in response to the temperature stress of U. prolifera was associated with miR-2916/PCNA/CyclinA/MAPK pathway. In conclusion, the study preliminarily illuminates the molecular mechanism in response to temperature stress of U. prolifera, and may provide a new insight for prevention of green tide.
On Use of Bivariate Survival Models with Cure Fraction

Correlated Gamma Frailty Model In our original article, we proposed the methodology in the very general setting of copula model (Genest and Mackay, 1986; Marshall and Olkin, 1988). We illustrated the application of the methodology using three specific distribution of the general class, namely Clayton's (1978), Frank's (1979), and Stable family (Hougaard, 1986). It is true that all of these three models correspond to an underlying shared frailty model. The class of Copula models, however, are much more general and can include correlated frailty models. In fact, the correlated frailty model the authors proposed to use as an extension of our methodology is a special case of the copula model with the copula function given by
Comparison of spectral and finite element methods applied to the study of the core‐annular flow in an undulating tube

A Galerkin/finite element and a pseudo‐spectral method, in conjunction with the primitive (velocity‐pressure) and streamfunction‐vorticity formulations, are tested for solving the two‐phase flow in a tube, which has a periodically varying, circular cross section. Two immiscible, incompressible, Newtonian fluids are arranged so that one of them is around the axis of the tube (core fluid) and the other one surrounds it (annular fluid). The physical and flow parameters are such that the interface between the two fluids remains continuous and single‐valued. This arrangement is usually referred to as Core‐Annular flow. A non‐orthogonal mapping is used to transform the uneven tube shape and the unknown, time dependent interface to fixed, cylindrical surfaces. With both methods and formulations, steady states are calculated first using the Newton–Raphson method. The most dangerous eigenvalues of the related linear stability problem are calculated using the Arnoldi method, and dynamic simulations are carried out using the implicit Euler method. It is shown that with a smooth tube shape the pseudo‐spectral method exhibits exponential convergence, whereas the finite element method exhibits algebraic convergence, albeit of higher order than expected from the relevant theory. Thus the former method, especially when coupled with the streamfunction‐vorticity formulation, is much more efficient. The finite element method becomes more advantageous when the tube shape contains a cusp, in which case the convergence rate of the pseudo‐spectral method deteriorates exhibiting algebraic convergence with the number of the axial spectral modes, whereas the convergence rate of the finite element method remains unaffected. Copyright © 2002 John Wiley & Sons, Ltd.
Satellite‐based ET estimation in agriculture using SEBAL and METRIC

Surface Energy Balance Algorithms for Land (SEBAL) and Mapping EvapoTranspiration at high Resolution with Internalized Calibration (METRIC) are satellite‐based image‐processing models that calculate evapotranspiration (ET) as a residual of a surface energy balance. Both models are calibrated using inverse modelling at extreme conditions approach to develop image‐specific estimations of the sensible heat flux (H) component of the surface energy balance and to effectively remove systematic biases in net radiation, soil heat flux, radiometric temperature and aerodynamic estimates. SEBAL and METRIC express the near‐surface temperature gradient as an indexed function of radiometric surface temperature, eliminating the need for absolutely accurate surface temperature and the need for air temperature measurements. Slope and aspect functions and temperature lapsing are used in METRIC applications in mountainous terrains. SEBAL and METRIC algorithms are designed for relatively routine application by trained professionals familiar with energy balance, aerodynamics and basic radiation physics. The primary inputs for the models are short‐wave and long‐wave (thermal) images from satellite (e.g. Landsat and MODIS), a digital elevation model and ground‐based weather data measured within or near the area of interest. ET ‘maps’ (i.e. images) developed using Landsat images provide means to quantify ET on a field basis in terms of both rate and spatial distribution. METRIC takes advantage of calibration using weather‐based reference ET so that both calibration and extrapolation of instantaneous ET to 24‐h and longer periods compensate for regional advection effects where ET can exceed daily net radiation. SEBAL and METRIC have advantages over conventional methods of estimating ET using crop coefficient curves or vegetation indices in that specific crop or vegetation type does not need to be known and the energy balance can detect reduced ET caused by water shortage, salinity or frost as well as evaporation from bare soil. Copyright © 2011 John Wiley & Sons, Ltd.
Instantaneous magnetic field distribution in brushless permanent magnet DC motors. I. Open-circuit field

An analytical technique for predicting the instantaneous magnetic field distribution in the airgap region of radial-field topologies of brushless permanent-magnet DC motors, under any specified load condition and accounting implicitly for the stator winding current waveform and the effect of stator-slot-openings, has been developed. It is based on the superposition of the component fields due to the permanent magnet and the stator excitation. A 2D analytical method for predicting the open-circuit airgap field distribution in both internal and external rotor radial-field motor topologies is presented. It involves the solution of the governing field equations in polar coordinates in the annular airgap/magnet region of a multipole slotless motor in which the magnets are assumed to have uniform radial magnetization and a constant relative recoil permeability. Results for various radial-field motors are compared with predictions from corresponding finite element analyses. >