Miracle-dz/UniFAR-FTUs huggingface dataset:
Conditional Cooperativity of Toxin - Antitoxin Regulation Can Mediate Bistability between Growth and Dormancy

Many toxin-antitoxin operons are regulated by the toxin/antitoxin ratio by mechanisms collectively coined “conditional cooperativity”. Toxin and antitoxin form heteromers with different stoichiometric ratios, and the complex with the intermediate ratio works best as a transcription repressor. This allows transcription at low toxin level, strong repression at intermediate toxin level, and then again transcription at high toxin level. Such regulation has two interesting features; firstly, it provides a non-monotonous response to the concentration of one of the proteins, and secondly, it opens for ultra-sensitivity mediated by the sequestration of the functioning heteromers. We explore possible functions of conditional regulation in simple feedback motifs, and show that it can provide bistability for a wide range of parameters. We then demonstrate that the conditional cooperativity in toxin-antitoxin systems combined with the growth-inhibition activity of free toxin can mediate bistability between a growing state and a dormant state.
Flux through Individual Muscle Acetylcholine Receptor Channels

We describe an optical technique using total internal reflection fluorescence (TIRF) microscopy to obtain simultaneous and independent recordings from numerous ion channels via imaging of single-channel Ca 2 flux. Muscle nicotinic acetylcholine (ACh) receptors made up of subunits were expressed in Xenopus oocytes, and single channel Ca 2 fluorescence transients (SCCaFTs) were imaged using a fast (500 fps) electron-multiplied c.c. d. camera with fluo-4 as the indicator. Consistent with their arising through openings of individual nicotinic channels, SCCaFTs were seen only when a nicotinic agonist was present in the bathing solution, were blocked by curare, and increased in frequency as roughly the second power of [ACh]. Their fluorescence amplitudes varied linearly with membrane potential and extrapolated to zero at about 60 mV. The rise and fall times of fluorescence were as fast as 2 ms, providing a kinetic resolution adequate to characterize channel gating kinetics; which showed mean open times of 7.9 and 15.8 ms when activated, respectively, by ACh or suberyldicholine. Simultaneous records were obtained from 400 channels in the imaging field, and we devised a novel “channel chip” representation to depict the resultant large dataset as a single image. The positions of SCCaFTs remained fixed ( 100 nm displacement) over tens of seconds, indicating that the nicotinic receptor/channels are anchored in the oocyte membrane; and the spatial distribution of channels appeared random without evidence of clustering. Our results extend single-channel TIRFM imaging to ligand-gated channels that display only partial permeability to Ca 2 , and demonstrate an order-of-magnitude improvement in kinetic resolution. We believe that functional single-channel imaging opens a new approach to ion channel study, having particular advantages over patch-clamp recording in that it is massively parallel, and provides high-resolution spatial information that is inaccessible by electrophysiological techniques.
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Thus, ecological effects are important to understanding children's reading development. As such, our study was guided by an ecological developmental approach. Bronfenbrenner and Morris (2006) contended that an ecological developmental approach is served by the four constructs triggering growth and change in academic competence, namely person, process, context, and time. The present study focused on three constructs: person, process, and context, all of which directly influence children's development. Person indicates child characteristics such as prior reading skills and family SES. Process represents the activities or interactions in which children are engaged in. Context indicates the environment and its associated learning opportunities (Ponitz et al., 2009). In this study, children's engagement represented process ; classroom quality (quality of teacher–child interactions) was used as an indicator of context and children's SES and prior literacy skills were used as indicators of person. Time is captured indirectly by the longitudinal design of the study. The ecological developmental approach emphasizes the importance of interrelationships among person, process, and context when studying children's development. Rather than examining individual contributions of each construct, the ecological framework suggests that researchers also attend to the interactive effects among these constructs (Bronfenbrenner, 1979). In fact, researchers have attempted to examine the interactive process between process and context in predicting children's learning. Specifically, context (teacher–child interactions) promotes child achievement indirectly through positive association with process (children's engagement; Ponitz et al., 2009). In the current study, we aimed to expand the existing literature by examining the individual influences of process (children's engagement) and context (teacher–child interactions)
De novo Transcriptome Assembly and SNP Discovery Pogonus chalceus (Coleoptera, Carabidae)

Background: The salt marsh beetle Pogonus chalceus represents a unique opportunity to understand and study the origin and evolution of dispersal polymorphisms as remarkable inter-population divergence in dispersal related traits (e.g. wing development, body size and metabolism) has been shown to persist in face of strong homogenizing gene flow. Sequencing and assembling the transcriptome of P. chalceus is a first step in developing large scale genetic information that will allow us to further study the recurrent phenotypic evolution in dispersal traits in these natural populations. Methodology/Results: We used the Illumina HiSeq2000 to sequence 37 Gbases of the transcriptome and performed de novo transcriptome assembly with the Trinity short read assembler. This resulted in 65,766 contigs, clustering into 39,393 unique transcripts (unigenes). A subset of 12,987 show similarity (BLAST) to known proteins in the NCBI database and 7,589 are assigned Gene Ontology (GO). Using homology searches we identified all reported genes involved in wing development, juvenileand ecdysteroid hormone pathways in Tribolium castaneum. About half (56.7%) of the unique assembled genes are shared among three life stages (third-instar larva, pupa, and imago). We identified 38,141 single nucleotide polymorphisms (SNPs) in these unigenes. Of these SNPs, 26,823 (70.3%) were found in a predicted open reading frame (ORF) and 6,998 (18.3%) were nonsynonymous. Conclusions: The assembled transcriptome and SNP data are essential genomic resources for further study of the developmental pathways, genetic mechanisms and metabolic consequences of adaptive divergence in dispersal power in natural populations. Citation: Van Belleghem SM, Roelofs D, Van Houdt J, Hendrickx F (2012) De novo Transcriptome Assemb and SNP Discovery in the Wing Polymorphic Salt Marsh Beetle Pogonus chalceus (Coleoptera, Carabidae). PLoS ONE 7(8): e42605. doi:10.1371/journal.pone. 0042605 Editor: Zhanjiang Liu, Auburn University, United States of America Received May 17, 2012; Accepted July 9, 2012; Published August 1, 2012 Copyright: 2012 Van Belleghem et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: Funding was received from the FWO-Flanders (PhD grant to Steven Van Belleghem) and the Belgian Science Policy (MO/36/025) and partly conducted within the framework of the Interuniversity Attraction Poles programme IAP (SPEEDY) – Belgian Science Policy. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: Steven.VanBelleghem@UGent.be
STUDIES ON T H E MODE OF A C T I O N OF D I P H T H E R I A I. I~OSPEOR~rE~ I~¢rER~mDIATES IN N O e L

I t was shown by Strauss and Hendee (1) that when purified diphtheria toxin was added to cultures of HeLa cells to a level of 0.5 t~g per ml or greater, incorporation of S85-methionine into cell protein continued at a normal rate for 1.5 to 2 hours and then ceased abruptly. In the presence of lower concentrations of toxin, protein synthesis continued at its normal rate for a longer period before coming to a standstill. These findings were confirmed by Kato and Pappenheimer (2) who observed a simultaneous reduction in the rate of ribonucleic acid formation. Kato and Pappenheimer also reported that within a few minutes after addition of a saturating dose of toxin to cultures of either human M K ceils or HeLa cells growing in the presence of glucose, there was a 40 per cent inhibition in the "steady state" level of incorporation of inorganic phosphate into adenine nucleotides. They suggested that diphtheria toxin acts reversibly at the cell surface where it interferes in some way with cytochromelinked phosphorylation concerned with transport of inorganic phosphate across the cell membrane. I t was postulated that this in turn leads to the arrest of protein synthesis. Strauss (3), working independently, also observed some decrease in nucleic acid synthesis following the arrest of protein synthesis in intoxicated ceils. However, he was unable to demonstrate any significant difference between normal and intoxicated cells in the kinetics of incorporation of inorganic P~ into nucleotides over a period of at least 120 minutes following the addition of a saturating dose of toxin. If inhibition of protein synthesis in toxin-treated mammalian cells is, in
Generation of arbitrary higher order Poincaré beams from a visible metasurface laser

The use of beams carrying orbital angular momentum (OAM) has become ubiquitous and topical in a variety of research fields. More recently, there has been a growing interest in exotic OAM carrying beams with spatially variant polarisation, so called Poincaré sphere beams. Structuring these beams at the source gives rise to compact solutions for a myriad of applications, from laser materials processing to microscopy. Here we present a visible laser that control's the angular momentum of light by arbitrary spin-orbit (SO) momentum conversion using novel metasurface devices. Further, we outline how to generate high purity OAM states in a deterministic manner with charge up to 100. Finally, we demonstrate the generation of symmetric and non-symmetric vector vortex beams from the same source with a large OAM differential between modes of up to 90. The performance and versatility in design of our approach offers a route to control light's angular momentum at the source.
Electro-optic based adiabatic frequency conversion in a non-centrosymmetric microresonator

A rather unknown method to perform optical frequency tuning is the adiabatic frequency conversion. But this method has some appealing advantages compared to conventional frequency conversion schemes, i. e. nonlinear- optical based ones: The internal conversion efficiency can reach unity even on a single-photon level. No threshold and no phase-matching conditions need to be fulfilled. Previous realizations of adiabatic frequency conversion suffer from short photon lifetimes, limited tuning range and challenging experimental setups. Here, we employ the Pockels effect for adiabatic frequency conversion (AFC) in a non-centrosymmetric ultrahigh-Q microresonator made out of lithium niobate. With a 70-μm-thick resonator we observe frequency shifts of more than 5 GHz by applying a moderate voltage of 20V. In contrast to former schemes our setup is considerably simplified and provides a linear electric-to-optical link that enables us to generate also arbitrary waveforms of frequency shifts. Furthermore, our presented conversion scheme is well-suited for on-chip fabrication. Volume fabrication and application of larger electric fields for reasonable voltages become possible. By doing this, it is feasible to achieve tuning on the order of hundreds of GHz.
Simultaneous enhancement of dynamic range and sensitivity in slope-assisted Brillouin optical time-domain analyzers via gain spectrum engineering

Brillouin spectrum engineering for the enhancement of slope-assisted Brillouin dynamic sensing is investigated by simulation. By superimposing the Brillouin gain with Brillouin losses, the tradeoff between the dynamic range and the frequency-to-amplitude sensitivity becomes more flexible. Compared to a conventional dynamic Brillouin sensor, a simultaneous enhancement of the dynamic range by 60.27% and the sensitivity by 51.21% has been achieved with the proper parameters. Due to these enhancements, the proposed sensor is 33.87% more robust to system noise and provides a more than 2.2 times of accuracy improvement for strain signal recovery.
Impact of light and ambient gas on the resistance of sputter-deposited non-doped ZnO films

This paper demonstrates the impacts of light and ambient gas on the resistance of sputter-deposited non-doped ZnO films. Although the authors have already demonstrated the impact of light from various LEDs with a different wavelength on the resistance of such films, key results were not shown in detail. In this paper, the influence of ambient gas on the resistance and the influence of temperature on resistance are demonstrated in detail, and feasible physics drawn from analysis results are discussed. Physical images of the phenomena are proposed. It is also comprehensively revealed that the film surface condition significantly contributes to the transport characteristics of the film; this is supported by the impact of ambient gas in the dark on the current decay process in the film.
Developments of high power blue diode laser systems for laser metal deposition and welding of pure copper materials

Pure copper processing is widely demanded in automobile, aerospace and electrical industries and so on since pure copper has excellent properties such as thermal and electrical conductivities. However, high quality welding and cladding of pure copper with near infrared lasers such as fiber, disk and diode lasers have not been performed yet. Their absorption rates of them for pure copper were less than 10 %. Therefore, we focused on blue (450 nm) diode laser with its absorption rate for pure copper of about 60 %. In this paper, we reported development of high power blue diode lasers for welding and additive manufacturing including cladding.
On-product focus monitoring and control for immersion lithography in 3D-NAND manufacturing

The market transition from 2D to 3D-NAND in recent years requires strict focus control and monitoring solutions. ASML’s μDBF targets (micro Diffraction Based Focus) enable on-product focus measurement which can be used to optimize scanner correction. Additionally, dense computational focus maps can be generated by combining μDBF measurements with scanner metrology such as non-correctable leveling error. This paper discusses the focus variability observed on memory layers through on product focus monitoring. This work will show how exposure at best focus can be performed for immersion lithography in the case of strong focus fingerprints. Focus monitoring data from μDBF and computational focus metrology will be used to generate and apply corrections on two 3D-NAND layers.
Calibration of a MOx-specific EUV photoresist lithography model

MOx resists have matured into promising alternatives to conventional CAR resists for advanced-node EUV lithography where these materials offer potential improvements to patterning fidelity and high etch resistance based on metallic components. This is a particular boon for processes with limited exposure latitudes such as High-NA EUV lithography. Creating and employing first-principle models of MOx lithographic processes should speed adoption and development of these materials and represents an important aspect of platform maturation. Stochastic photochemical models of metalcontaining resist systems have previously been developed, but without extension to computational lithography. Likewise, stochastic models derived from CAR systems have been fit to MOx lithographic data using computational lithography software, facilitating limited stochastic lithography studies without capturing fundamental MOx imaging processes. Recently, a rigorous stochastic model built from the ground up using MOx-specific resist principles has been developed. In this contribution, the performance of this MOx-specific model was assessed by comparing simulated and experimental lithography data for a series of MOx resists under a range of exposure and process conditions. Chemical and physical properties of the resists derived independently from X-ray diffraction, EUV absorbance, FTIR spectroscopy, and ellipsometry measurements were parameterized in the context of the simulation, and calibration routines were used to fit simulated data to experimental CD-SEM exposure data produced using an NXE-3300B EUV scanner. Insights from these models may be used to guide MOx resist development and EUV lithography process optimization. Ultimately, these studies will help to identify process windows, processing points, and possibly improvements to the MOx resists.
Characterization of Microsatellite Loci for an Endangered Plant, Warea amplexifolia.

Abstract. Clasping Warea (Warea amplexifolia) is a critically endangered plant species endemic to Florida. It is threatened due to habitat loss through urban development and poor land management, resulting in habitat fragmentation and small population sizes. To aid recovery strategies, information is needed on the genetic diversity among and within populations. We identified fourteen microsatellite loci that were polymorphic in W. amplexifolia and in the related W. sessilifolia, and nine loci that were polymorphic in W. cuneifolia. In W. amplexifolia, the number of alleles per microsatellite locus varied between four and 15, with observed heterozygosity in the range of 0.10 to 0.73. These newly identified markers will be used to inform recovery efforts for W. amplexifolia and may also be useful for studies of the population genetics of closely related taxa.
High-power, high-beam quality miniaturized laser module for pumping of solid state lasers at 980 nm

This work presents a miniaturized laser module featuring an optical output power of more than 14Win continuous wave operation. Simultaneously, a beam quality factor of less than 2 is reached at the operating power. The laser module layout is based on the use of tapered diode lasers featuring wavelength stabilization by a monolithic distributed Bragg grating. Such a single laser source achieves a reliable output power in the order of 8W in continuous wave mode at a wavelength of 980nm [1]. To enhance the output power while maintaining the beam quality of the single emitters, two laser beams were combined by the use of polarization coupling. The use of custom designed beam couplers is necessary to combine the given radiation intensities. A thin film polarization optic, adapted to the output wavelength was used. All optical components where designed to be housed inside of a module with a footprint of 58 x 34mm2. Due to the close spatial vicinity of the laser sources, thermal simulations were carried out to avoid thermal crosstalk and ensure stable laser operation. The modules high beam quality enables pumping of solid state lasers and amplifiers even without challenging optical pumping geometries.
Investigation of single-mode anti-resonant hollow-core THz fibers

Single-mode fiber plays an important role in the applications of THz technology. Serving as one of the optimal choices of THz fiber, hollow-core anti-resonant fiber (ARF) with single-layer anti-resonant elements has advantages of low transmission loss, high damage threshold, low dispersion but disadvantage of single mode which can by realized by the high-order-mode (HOM) suppression effect. In this paper, the key factor affecting the HOM suppression effect in THz ARF is investigated and confirmed to be the cross-sectional area ratio of cladding tubes inner side with fiber core, besides, the ratio will slightly change with the variation of the anti-resonant period of THz ARF where the cladding tubes have different shell thickness. By optimizing the anti-resonant elements of THz ARF from round tubes to semielliptical tubes, a high-performance single-mode THz fiber is proposed and the confinement loss of high-order-mode is confirmed larger than 24 dB/m at the same time that of fundamental-mode is controlled less than 0.4 dB/m.
Nanostructures and design challenges in photovoltaic devices

Nanostructures play an important role in state-of-the-art photovoltaic devices. Optical and electrical characteristics of the devices can be improved with properly designed and fabricated nanotextures. In this contribution, we highlight examples of possible fabrication of nanotextures by using UV nanoimprinted lithography, their optical characterization by camera based angular resolved spectroscopy and perform computer-assisted design of nanotextures for best optical performance of heterojunction silicon and ultra-thin chalcopyrite solar cells.
High brightness MOCVD-grown laser diodes using RPCVD tunnel junctions

The unique growth conditions of BluGlass’ low growth temperature technology Remote Plasma Chemical Vapour Deposition (RPCVD) are capable of producing Activate As-Grown (AAG) buried p-GaN layers. This ability renders RPCVD a highly attractive technique to produce GaN-based Tunnel Junctions (TJ) without the complexities associated with the post-growth lateral activation steps required by MOCVD. In this paper we discuss the use of hybrid RPCVD/MOCVD TJs for MOCVD-grown ridge guide laser diode (LD) applications. The impact of both the structure and placement of the TJ on the total optical loss of the LD are investigated. TJs conforming to the strict compositional requirements in order to yield a net reduction in optical loss are demonstrated, paving the way to improved conversion efficiencies through the replacement of the highly resistive p-AlGaN cladding layers and p-type Ohmic contacts with lower resistance n-AlGaN cladding layers and n-type Ohmic contacts.
Nanoparticles as Versatile Tools for Mechanotransduction in Tissues and Organoids

Organoids are 3D multicellular constructs that rely on self-organized cell differentiation, patterning and morphogenesis to recapitulate key features of the form and function of tissues and organs of interest. Dynamic changes in these systems are orchestrated by biochemical and mechanical microenvironments, which can be engineered and manipulated to probe their role in developmental and disease mechanisms. In particular, the in vitro investigation of mechanical cues has been the focus of recent research, where mechanical manipulations imparting local as well as large-scale mechanical stresses aim to mimic in vivo tissue deformations which occur through proliferation, folding, invagination, and elongation. However, current in vitro approaches largely impose homogeneous mechanical changes via a host matrix and lack the required positional and directional specificity to mimic the diversity of in vivo scenarios. Thus, while organoids exhibit limited aspects of in vivo morphogenetic events, how local forces are coordinated to enable large-scale changes in tissue architecture remains a difficult question to address using current techniques. Nanoparticles, through their efficient internalization by cells and dispersion through extracellular matrices, have the ability to provide local or global, as well as passive or active modulation of mechanical stresses on organoids and tissues. In this review, we explore how nanoparticles can be used to manipulate matrix and tissue mechanics, and highlight their potential as tools for fate regulation through mechanotransduction in multicellular model systems.