Miracle-dz/UniFAR-FTUs huggingface dataset:
An Engineer's View on Regulation of Seed Development

The recently proposed Systems Biology Graphical Notation (SBGN) represents a flexible system of nomenclature for the description of biological networks, comparable to the notation employed by designers of electronic circuits. It allows the uniform and unambigu-ous display of complex biological information. Here we present an application of SBGN to describe processes occurring during seed development in Arabidopsis thali-ana. Representative network maps can be accessed via the open resource RIMAS web portal. Circuit maps in biology A uniform system of nomenclature describing the components of networks and based on a well-defined set of symbols, is well established within the engineering field, as it greatly facilitates communication efficiency and clarity. In biology, equivalent notation systems have been suggested [1–3], but have as yet failed to become accepted as a common standard due to several shortcomings. A concerted effort mounted by a major consortium of biological network specialists has now proposed the 'Systems Biology Graphical Notation' (SBGN, see Glossary and www.sbgn.org) scheme [4]. SBGN incorporates a limited number of 33 easily recognizable glyphs, and can be used to represent a broad range of biological networks, including metabolic pathways and transcriptional regulatory circuits. It can incorporate structural, non-dynamic information , and thereby simplifies further network analyses (e.g. based on data mapping). A range of supporting software tools has also been developed (www.sbgn.org). To accommodate different informational aspects of the same network and to permit network visualization at various levels of granularity, SBGN allows for the use of three independent languages: 'Process Description' (PD), 'Entity Relationship' (ER)' and 'Activity Flow' (AF). The PD view describes a sequence of processes as transitions of entities from one state to another. In contrast, the ER language focuses on the interactions of entities without considering their temporal course. Finally, the AF notation allows the conceptual visualization of information fluxes (such as modulation, inhibition or stimulation) between entities. Thus, SBGN provides a uniform basis for the representation of complex biological systems, and has the potential to be widely accepted and routinely applied. To demonstrate the performance of SBGN, we show here an application based on the PD language, to represent much of the current understanding of the regulatory processes underpinning seed development in Arabidopsis (Arabidopsis thaliana) [5–7]. Network maps can be accessed online from the RIMAS (Regulatory Interaction Maps of Arabidopsis Seed Development) portal (see Box 1), which focuses on hierarchical transcriptional regulation, and hormonal and epigenetic factors. As an …
Elliptic Fourier shape analysis of fossil bivalves: some practical considerations

Elliptic Fourier shape analysis is a powerful, though under-utilized, biometric tool that is particularly suited for the description of fossils lacking many homologous landmarks, such as several common bivalve groups. The method is conceptually more parsimonious than more traditional biometric methods based on discrete linear and angular measurements. Most importantly, however, shape analysis captures a much higher proportion of the morphological information resident in any fossil than analyses based on discrete measurements. The number of harmonics required in an elliptic Fourier analysis can be estimated from a series of inverse Fourier reconstructions, or from the power spectrum. In most studies it is appropriate to normalize Fourier coefficients for size, although this information can be reincorporated at a later stage. The coefficients should probably not be standardized, unless there is evidence to suggest that high-frequency information was genetically as important as low-frequency information. Depending upon the aims of a particular study and the morphological disparity of the fossils in question, it might be appropriate to eliminate the first harmonic (‘best-fitting’) ellipse from an analysis. Meaningful comparison of the left and right valves of bivalves requires the digitized coordinates of one or other to be mirrored prior to computation of the Fourier coefficients. □Biometric analysis, Bivalvia, elliptic Fourier analysis, morphometrics.
Experimental tuning of transport regimes in hyperuniform disordered photonic materials

This document contains the scattering properties of a single rod, details on the structures of the point patterns, the band structure calculation, details on the time domain propagation videos and all the technical information on the data analysis. The seven videos show how the electromagnetic wave propagates in the cavity for di(cid:27)erent frequency ranges (see Supplemental Material Fig. S6 for the description of the videos).
Role of simulated GOSAT total column CO2 observations in surface CO2 flux uncertainty reduction

[1] We investigated the utility of Greenhouse Gases Observing Satellite (GOSAT) column CO2 observations in surface CO2 flux estimation. We addressed two key issues in carbon flux estimation from satellite data: (1) reduction of the CO2 flux uncertainty and (2) bias in the constrained surface fluxes. Our results showed that GOSAT data with 1.7 ppm precision (monthly mean, land observation only) had the same utility as observational data from the existing surface network. By adding satellite observations with 2.5 ppm single-shot random error and a bias of 1 ppm, it was possible to reduce the mean regional flux uncertainty by approximately 30%. Unbiased data with 2.5 ppm single-shot precision (0.8 ppm for the monthly mean) halved the flux uncertainty. The aerosol-dependent bias in satellite data with 1 ppm mean variance led to significant absolute errors in the surface CO2 fluxes, highlighting a need for the accurate detection and rejection of biased data.
High-throughput fluorescence-based screen identifies the neuronal 1 microRNA miR-124 as a positive regulator of alphavirus infection

Micro (mi)RNAs are small regulatory RNAs, which act by modulating the expression of 26 target genes. In addition to their role in maintaining essential physiological functions in the 27 cell, miRNAs can also regulate viral infections. They can do so directly by targeting RNAs of 28 viral origin or indirectly by targeting host mRNAs and this can result in a positive or negative 29 outcome for the virus. Here, we performed a fluorescence-based miRNA genome-wide screen 30 in order to identify cellular miRNAs involved in the regulation of arbovirus infection in 31 human cells. We identified sixteen miRNAs showing a positive effect on Sindbis virus 32 (SINV) expressing GFP, among which a number of neuron-specific ones such as miR-124. 33 We confirmed that overexpression of miR-124 increases both SINV structural protein 34 translation and viral production and that this effect is mediated by its seed sequence. We 35 further demonstrated that the SINV genome possesses a binding site for miR-124. Both 36 inhibition of miR-124 or silent mutations to disrupt this binding site in the viral RNA 37 abolished the positive regulation. We also proved that miR-124 inhibition reduces SINV 38 infection in human differentiated neuronal cells. Finally, we showed that the proviral effect of 39 miR-124 is conserved for other alphaviruses as its inhibition reduces chikungunya virus 40 (CHIKV) viral production in human cells. Altogether, our work expands the panel of positive 41 regulation of the viral cycle by direct binding of host miRNAs to the viral RNA and provides 42 new insights into the role of cellular miRNAs as regulators of alphavirus infection. regulates the virus by increasing viral structural protein translation and viral production, and we identified a binding site for this small RNA in the viral genome. miR-124 is the most expressed, conserved and specific microRNA in the central nervous system (CNS) and it has been described as a master regulator of neuronal differentiation (27). It is up-regulated as neuronal progenitors exit mitosis and begin to differentiate (28) and its expression has been shown to be sufficient to drive cells into the neuronal pathway (29). Mutations in the miR-124 seed region or in the binding site on the viral RNA abolished the regulation. We also proved that the miR-124 inhibition strategy via antisense oligonucleotides reduces both SINV and CHIKV production in human cells expressing this miRNA. These studies highlight a novel role for miR-124 in arbovirus infection and suggest that targeting alphavirus infection via miRNA modulation could be used therapeutically.
Hypoxia-Induced Neonatal Seizures Diminish Silent Synapses and Long-Term Potentiation in Hippocampal CA1 Neurons

Neonatal seizures can lead to epilepsy and long-term cognitive deficits into adulthood. Using a rodent model of the most common form of human neonatal seizures, hypoxia-induced seizures (HS), we aimed to determine whether these seizures modify long-term potentiation (LTP) and silent NMDAR-only synapses in hippocampal CA1. At 48–72 h after HS, electrophysiology and immunofluorescent confocal microscopy revealed a significant decrease in the incidence of silent synapses, and an increase in AMPARs at the synapses. Coincident with this decrease in silent synapses, there was an attenuation of LTP elicited by either tetanic stimulation of Schaffer collaterals or a pairing protocol, and persistent attenuation of LTP in slices removed in later adulthood after P10 HS. Furthermore, postseizure treatment in vivo with the AMPAR antagonist 2,3-dihydroxy-6-nitro-7-sulfonyl-benzo[f]quinoxaline (NBQX) protected against the HS-induced depletion of silent synapses and preserved LTP. Thus, this study demonstrates a novel mechanism by which early life seizures could impair synaptic plasticity, suggesting a potential target for therapeutic strategies to prevent long-term cognitive deficits.
An Insight into Molecular Scale Interactions and In-situ Nanomechanical Properties of Kerogen in Green River Oil Shale

Green river oil shale located in the western states of Colorado, Utah and Wyoming in the United States are reported to be among the richest potential source of crude oil in the world. It is estimated that in the United States, these rocks contain approximately two trillion barrel equivalent of crude oil, of which about 800 billion barrels are accessible. Due to the relatively young age of these rocks, (about 54 million years) the organic phases in these rocks are precursors to crude oil called kerogen. Some of the current pilot-scale techniques that attempt to extract kerogen are through retorting techniques that involve heating the rock to high temperatures. This technique is not commercially viable due to the large energy cost incurred in extracting hydrocarbons, and the emissions associated with the retorting process. An in-depth study to understand how kerogen is “locked” in the shale matrix has been undertaken by the authors. This paper presents the experimental investigation of Green River Oil Shale samples using microscopy, infrared spectroscopy and nanoindentation techniques. Green river oil shale samples were obtained from a depth of approximately 570 feet. Samples were cut from the rock cores for experimental investigation. Photoacoustic fourier transform infrared spectroscopy tests revealed that the light colored regions of the rock have more kerogen than the dark regions. In addition, significant influence of molecular interactions with the mineral phase seems to alter the kerogen phase. Electron microscopy studies in combination with EDS revealed that the kerogen- rich phases are much smaller in size than that reported in literature and this will have significant ramifications on the behavior of in-situ kerogen. Extensive nanoindentation tests on the oil shale samples allow for studying the response of the mineral phase and the in-situ kerogen phase,
Indentor‐corner tectonics in the Yakutat‐St. Elias collision constrained by GPS

The Yakutat‐St. Elias collision in SE Alaska and adjacent Canada represents a prime example of present‐day tectonics associated with an indentor corner. Its eastern syntaxis is marked by high exhumation, a sharp structural bend, and strain concentration at the transition from shortening to oblique transpression. Here we present GPS velocity and strain rate fields that cover the syntaxis, including 11 new stations in the core of the St. Elias Mountains. These data are corrected for transient deformation (glacial isostatic adjustment and postseismic and interseismic loading) to produce residual velocities and strain rates representative of long‐term tectonics. The main features of these velocity and strain rate fields are a peak in strain rates (strain knot) in the syntaxis at the junction between the main fault systems and a rapid rotation from convergence‐parallel to convergence‐normal orientations of the velocities and shortening axes around the syntaxis, leading to shortening across the southern Denali Fault. These features are consistent with the strain and tectonic patterns expected near an indentor corner at the transition from shortening to transpression, with a combination of diffuse and localized deformation. The GPS velocities and strain rates show diffuse deformation around the syntaxis, from pure convergence‐parallel shortening in the orogenic wedge to oblique extension that accommodates the strain rotation at the front of the syntaxis. This indentor‐corner model also results in a near‐zero strike‐slip rate on the southern Denali Fault and shows no clear evidence for a throughgoing fault hypothesized to link the Fairweather and Totschunda Faults.
Stereotomography: a semi‐automatic approach for velocity macromodel estimation

Most methods for velocity macromodel estimation require considerable operator input, mainly concerning the regularization and the picking of events in the data set or in the migrated images. For both these aspects, slope tomography methods offer interesting solutions. They consider locally coherent events characterized by their slopes in the data cube. Picking is then much easier and consequently denser than in standard traveltime tomography. Stereotomography is the latest slope tomography method. In recent years it has been improved significantly, both from an algorithmic point of view and in terms of practical use. Robust and fast procedures are now available for 2D stereotomographic picking and optimization.
Exact elastic impedance in orthorhombic media

Conventional elastic/ray impedance approximations are derived as a scalar to heuristically present seismic reflectivity based on the assumptions of weak impedance, isotropic media, or weak anisotropic media. In this paper, we derive the exact elastic impedance tensors of qP- and qS-waves for orthorhombic media based on the stress-velocity law. They represent the unique mechanical properties of the medium, thus are called elastic mechanical impedance (EMI). The impedance tensor can be reduced for an isotropic medium with a vertical symmetry axis (VTI) or a horizontal axis (HTI). Because no assumptions are made during the derivation, the new impedance shows good accuracy at large angle and can be used to characterize unconventional reservoirs with strong anisotropy, such as shale gas and coal-bed methane reservoirs. An approximation of P-wave EMI is also discussed for a TI medium. It is expressed by vertical velocities and thus is applicable to seismic inversion and interpretation. Application tests on real log data and seismic data show the robust interpretation capability of EMI in lithology characterization compared with conventional impedances.
Elevated sulfate reduction in metal-contaminated freshwater lake sediments

Although sulfate-reducing prokaryotes have long been studied as agents of metals bioremediation, impacts of long-term metals exposure on biologically mediated sulfur cycling in natural systems remains poorly understood. The effects of long-term exposure to metal stress on the freshwater sulfur cycle were studied, with a focus on biologic sulfate reduction using a combination of microbial and chemical methods. To examine the effects after decades of adaptation time, a field-based experiment was conducted using multiple study sites in a natural system historically impacted by a nearby zinc smelter (Lake DePue, Illinois). Rates were highest at the most metals-contaminated sites (-35 {mu}mol/cm{sup 3}/day) and decreased with decreased pore water zinc and arsenic contamination levels, while other environmental characteristics (i.e., pH, nutrient concentrations and physical properties) showed little between-site variation. Correlations were established using an artificial neural network to evaluate potentially non-linear relationships between sulfate reduction rates (SRR) and measured environmental variables. SRR in Lake DePue were up to 50 times higher than rates previously reported for lake sediments and the chemical speciation of Zn was dominated by the presence of ZnS as shown by X-ray Absorption Spectroscopy (XAS). These results suggest that long-term metal stress of natural systems might alter the biogeochemicalmore » cycling of sulfur by contributing to higher rates of sulfate reduction. « less
Transcriptomic signatures related to the obesity paradox in patients with clear cell renal cell carcinoma: a retrospective cohort study

Background— Obesity is associated with an increased risk of developing clear cell renal cell carcinoma (ccRCC) but, paradoxically, with improved oncologic outcomes. As the biologic mechanisms underlying this association are poorly understood, our study aimed to identify transcriptomic differences in primary tumor or peritumoral adipose tissue between obese and normal weight patients. Methods— After confirming the inverse association between body mass index (BMI ≥ 30 vs < 30 kg/m 2 ) and mortality in three independent clinical cohorts including 453 metastatic ccRCC patients treated with first-line VEGF-directed therapy from the Phase III COMPARZ clinical trial, targeted immunotherapy using the Kaplan–Meier method and analyzed by log-rank test, we evaluated and validated primary tumor transcriptomic differences. We also compared gene expression differences in peritumoral adipose tissue from a prospectively collected cohort of patients with non-metastatic ccRCC. Wilcoxon rank-sum test was used to analyze significant differences in gene expression between groups and false discovery correction was performed using the Benjamini-Hochberg procedure. advantage experienced by obese ccRCC patients. The complex interplay between the ccRCC tumor and peritumoral adipose and treatment selection. Future studies are required to evaluate the cross-talk between peritumoral adipose tissue and RCC, impact of visceral fat inflammation on outcomes in patients receiving immunotherapy, and therapeutic interventions to address adverse components of body size (e.g., increased visceral fat).
Methods used to delineate groundwater source protection zones in England and Wales

Abstract Groundwater source protection zones (GPZs) are an integral part of land surface zoning within the Environment Agency’s Policy and Practice for the Protection of Groundwater. The methods and experience gained in delineating GPZs around 1000 groundwater sources in England and Wales are reviewed. The methods include: manual calculations, hydrogeological mapping, analytical and semi- analytical modelling and numerical modelling. The large numbers of sources within a diverse number of hydrogeological settings has led to a structured approach to selecting the GPZ method appropriate to each groundwater source. This includes consideration of the protected yield, data acquisition and formulation of a conceptual flow model. The GPZ methods also include consideration of parameter uncertainty. Further developments in GPZ delineation methods are required to cope with fissured/fractured groundwater flow and to exploit the results of transient groundwater models.
Ethynylation of Cysteines from Peptides to Proteins in Living Cells

: Efficient methods to introduce bioorthogonal groups, such as terminal alkynes, into biomolecules are important tools for chemical biology. State-of-the-art approaches are based on the introduction of a linker between the targeted amino acid and the alkyne, and still present limitations of either reactivity, selectivity or adduct stability. Herein, we present an ethynylation method of cysteine residues based on the use of ethynylbenziodoxolone (EBX) reagents. In contrast to other approaches, the acetylene group is directly introduced onto the thiol group of cysteine and can be used in one-pot in a copper-catalyzed alkyne-azide cycloaddition (CuAAC) for further functionalization. Labeling proceeded with reaction rates comparable or higher than the most often used iodoacetamide on peptides or maleimide on the antibody trastuzumab. Under optimized conditions, high cysteine selectivity was observed. The reagents were also used in living cells for cysteine proteomic profiling and displayed an improved coverage of the cysteinome compared to previously reported iodoacetamide or hypervalent iodine-reagent based probes. Fine-tuning of the EBX reagents allowed optimization of their reactivity and physical properties for the desired application.
Petrogenesis of melt rocks, Manicouagan Impact Structure, Quebec

Abstract. The 65-km-diameter Manicouagan impact structure has an eroded 230-m-thick sheet of clast-laden, impact melt rock with an estimated preerosional volume of >270 km3. All samples are characterized by mineral and lithic clasts or their incompletely digested remnants. Drawing upon previous theoretical studies of shock waves, we suggest that the Manicouagan melt formed in 1 or 2 s in a 5-km-radius hemisphere near the point of impact. The melt accelerated to a few kilometers per second, and the melt and the less shocked debris surrounding it flowed downward and outward for a few minutes until the melt formed a lining of a 5- to 8-km-deep, 15- to 22-km-radius cavity. Extremely turbulent flow thoroughly homogenized the melt and promoted the incorporation and progressive digestion of slower moving, less shocked, cooler debris surrounding the melt. This debris had been finely fragmented, but not melted, to grain sizes of less than 1 mm by the passage of the shock waves. Because of the fine grain size, the melt and fragmented debris equilibrated thermally in about 100 s. During thermal equilibration, virtually all clastic debris (i.e. alkali feldspar, biotite, hornblende, garnet, and scapolite), other than highly refractory quartz and plagioclase as well as many of the centimeter size lithic clasts other than anorthosite, were digested. The preservation of quartz and plagioclase mineral clasts implies that the clasts and melt equilibrated to temperatures near but not above the liquidus. Plagioclase nucleation was initiated by the drop in temperature and possibly by direct nucleation on undigested debris. The initiation of crystallization vastly increased the melt viscosity, preventing settling of 10-mm clasts of basement. Flow of melt through basement fractures is evidence that readjustment of the crater floor took place during the period of clast-melt thermal equilibration.