gebhart/patrepeval huggingface dataset:
The Axial Element Protein DESYNAPTIC2 Mediates Meiotic Double-Strand Break Formation and Synaptonemal Complex Assembly in Maize (2015)

During meiosis, homologous chromosomes pair and recombine via repair of programmed DNA double-strand breaks (DSBs). DSBs are formed in the context of chromatin loops, which are anchored to the proteinaceous axial element (AE). The AE later serves as a framework to assemble the synaptonemal complex (SC) that provides a transient but tight connection between homologous chromosomes. Here, we showed that DESYNAPTIC2 (DSY2), a coiled-coil protein, mediates DSB formation and is directly involved in SC assembly in maize (Zea mays). The dsy2 mutant exhibits homologous pairing defects, leading to sterility. Analyses revealed that DSB formation and the number of RADIATION SENSITIVE51 (RAD51) foci are largely reduced, and synapsis is completely abolished in dsy2 meiocytes. Super-resolution structured illumination microscopy showed that DSY2 is located on the AE and forms a distinct alternating pattern with the HORMA-domain protein ASYNAPTIC1 (ASY1). In the dsy2 mutant, localization of ASY1 is affected, and loading of the central element ZIPPER1 (ZYP1) is disrupted. Yeast two-hybrid and bimolecular fluorescence complementation experiments further demonstrated that ZYP1 interacts with DSY2 but does not interact with ASY1. Therefore, DSY2, an AE protein, not only mediates DSB formation but also bridges the AE and central element of SC during meiosis.
Salivary isoprostanes indicate increased oxidation injury in periodontitis with additional tobacco abuse (2006)

Isoprostanes (IPs) are indicators of in-vivo oxidative stress, and have been successfully used as markers for chronic inflammatory processes. The presence of chronic periodontal disease and cigarette smoking has been individually linked to the development of atherosclerosis, yet data regarding oxidative stress in this context are not available yet. The aim of this study was to evaluate levels of the salivary prostaglandins (PGs) 8-epi-PGF(2alpha), 6-oxo-PGF(1alpha), thromboxane B(2) (TXB(2)) and PGF(2alpha) in association with periodontal disease status with and without additional cigarette smoking. We analyzed saliva samples from 121 adults, (aged 21-73 years, 90 non-smokers, 31 smokers) for levels of 8-epi-PGF(2alpha), 6-oxo-PGF(1alpha), TXB(2) and PGF(2alpha). On the basis of periodontal disease indices the periodontal status of each subject was assessed and outcomes were then correlated with smoking status and laboratory findings. Salivary 8-epi-PGF(2alpha) levels increased with deteriorating plaque index, and were significantly higher (115.5 +/- 23.5 pg/ml) in smoking individuals, when compared to non-smokers (70.2 +/- 20.4 pg/ml, p<0.0001). In addition, smokers showed higher TXB(2) and PGF(2alphas) and lower 6-oxo-PGF(1alpha) levels p<0.0001). Oxidative stress, as reflected by elevated salivary 8-epi-PGF(2alpha) levels, is associated with the extent of periodontal disease and is significantly aggravated by concomitant tobacco abuse. Chronic inflammation and smoking have been individually associated with the development of atherosclerosis. The results of this study indicate that: 1) salivary IPs can reliably assess the degree of oxidative stress, and: 2) smoking and periodontal disease are two modifiable cardiovascular risk factors, able to potentiate each other.
Conclusion : Travail, compétences et mondialisation (2011)

Spire est le dépôt institutionnel de la production scientifique de Sciences Po et contient le texte intégral des articles, ouvrages, chapitres d’ouvrages, working papers et communications dans des conférences de la communauté académique de Sciences Po.
Ensemble cell-wide kinetic modeling of anaerobic organisms to support fuels and chemicals production (2018)

The goal of this project is to understand the metabolism and underlying regulatory networks of two anaerobic microorganisms, Moorella thermoacetica and Clostridium thermocellum by making use of Ensemble Modeling (EM) paradigm through integration of multiple omic information (transcriptomic, proteomic, metabolomic & fluxomic). Kinetic models have the potential to provide a mechanistic description of cellular metabolism by combining several layers of regulatory events into an integrated framework. The foundation of the kinetic model is a stoichiometric network description. To this end, we have developed and curated genome-scale metabolic (GSM) models of the organisms that will serve as scaffold for building the kinetic models. For M. thermoacetica, the GSM model was constructed and tested by the Stephanopoulos group with experimental growth rate. The GSM elucidated the energy conservation mechanism under autotrophic growth conditions. For C. thermocellum, the Maranas group has developed the second-generation GSM model through integration of experimental data. The Maranas group has also constructed a core metabolic kinetic model of the organism which includes the central metabolism and all relevant pathways for biofuels production. The stoichiometric and kinetic model predictions were tested extensively using experimental data for wild-type and 20 mutant strains. We have outlined below in detail the progress related to specific individual aims. Below are listed publications of research carried out based on this research grant support.
Dynamic time reversal acoustic focusing of ultrasound for biomedical applications (2013)

Time Reversal Acoustic (TRA) system provides effective focusing in inhomogeneous media that can be used in various biomedical applications including high intensity ultrasound treatment, ultrasound-assisted drug delivery, ultrasonic battery charging of implants, etc. In many cases the temporal variation of propagating media properties leads to a degradation of the focusing. The in situ adjustment of radiated TRA signal is required in order to restore focusing. We present the feedback algorithm with Tikhonov regularization that enables the refocusing of acoustic field based on the changes in the focused signal received by a beacon. Temporal and spatial quality of the feedback refocusing was characterized experimentally using hydrophone and compared with standard TRA focusing. Algorithm is applicable for power delivery to implantable wireless cardiac pacemakers, percutaneous devices and neuro-stimulators.
Effect of polyamine depletion on c-myc expression in human colon carcinoma cells. (1988)

Polyamine depletion generally results in an inhibition of cell growth. However, the precise role of polyamines in the regulation of cell proliferation is unknown. In the present study, we demonstrate that polyamine depletion induced by 2-difluoromethylornithine in COLO 320 human colon carcinoma cells results in a greater than 90% decrease in expression of a key gene in the maintenance of cell growth, the c-myc protooncogene. The decrease in c-myc expression accompanying polyamine depletion appears to occur at the transcriptional level. It is not simply a result of decreased growth rate since growth-inhibited cells at confluence maintain a high level of c-myc expression. It is also due to a change in cell cycle phase distribution and is not a reflection of a generalized decrease in gene expression which accompanies a decrease in cellular proliferation. Thus, the expression of the histone H2A gene was similar to and temporally paralleled the growth status of both treated and untreated cells, while the beta-actin and ornithine decarboxylase genes actually had increased expression during polyamine depletion. These studies demonstrate that polyamines may be critical to the expression of c-myc and suggest one mechanism by which they modulate cell growth.
Inhibition of lung tumor growth by complex pulmonary delivery of drugs with oligonucleotides as suppressors of cellular resistance (2010)

Development of cancer cell resistance, low accumulation of therapeutic drug in the lungs, and severe adverse treatment side effects represent main obstacles to efficient chemotherapy of lung cancer. To overcome these difficulties, we propose inhalation local delivery of anticancer drugs in combination with suppressors of pump and nonpump cellular resistance. To test this approach, nanoscale-based delivery systems containing doxorubicin as a cell death inducer, antisense oligonucleotides targeted to MRP1 mRNA as a suppressor of pump resistance and to BCL2 mRNA as a suppressor of nonpump resistance, were developed and examined on an orthotopic murine model of human lung carcinoma. The experimental results show high antitumor activity and low adverse side effects of proposed complex inhalatory treatment that cannot be achieved by individual components applied separately. The present work potentially contributes to the treatment of lung cancer by describing a unique combinatorial local inhalation delivery of drugs and suppressors of pump and nonpump cellular resistance.
High-data-rate millimeter-wave subcarrier transmission using feedforward optical modulation (1994)

The ability to transmit millimeter-wave signals over fiber opens up new possibilities for distributed antenna networks and phased- array systems. Previous results have demonstrated the transmission of millimeter-wave signals at 40 Mbit/s around 35 GHz by using narrow-band resonant enhancement.1 In this paper we report a system demonstration of 300-Mbit/s binary-phase- shift-keyed (BPSK) signal transmission at a carrier frequency of 39 GHz through 2.2 km of optical fiber, using a recently reported feedforward modulation technique.2 A bit error rate (BER) of 10-9 at a received optical power of —9.8 dBm has been achieved. The experimental setup is shown in Fig. 1. The dotted enclosure represents the feedforward millimeter-wave optical modulator. Details of the operational principle of this modulation technique can be found in Ref. 2. In brief, a beat note at 36.5 GHz is generated by photomixing two 1.3-μιη distributed-feedback (DFB) lasers each with a free-running linewidth of 15 MHz and emitting at an optical power of 8 mW. The beat note is electrically-mixed with the input millimeter-wave signal that is centered at 39 GHz and contains pseudorandom (215 — 1) nonreturn-to-zero (NRZ) BPSK data at 150-300 Mbit/s. The resulting i.f. error signal at fD = 39.0 — 36.5 = 2.5 GHz is fed forward to an external optical modulator with a 4-GHz electrical bandwidth.
Features of MotA proton channel structure revealed by tryptophan-scanning mutagenesis. (1995)

The MotA protein of Escherichia coli is a component of the flagellar motors that functions in transmembrane proton conduction. Here, we report several features of MotA structure revealed by use of a mutagenesis-based approach. Single tryptophan residues were introduced at many positions within the four hydrophobic segments of MotA, and the effects on function were measured. Function was disrupted according to a periodic pattern that implies that the membrane-spanning segments are alpha-helices and that identifies the lipid-facing parts of each helix. The results support a hypothesis for MotA structure and mechanism in which water molecules form most of the proton-conducting pathway. The success of this approach in studying MotA suggests that it could be useful in structure-function studies of other integral membrane proteins.
Supplementary Figures S1-S9, Supplementary Table S1 from Limited Environmental Serine and Glycine Confer Brain Metastasis Sensitivity to PHGDH Inhibition (2023)

&lt;p&gt;Supplementary Figures and a Supplementary Table&lt;/p&gt;
Quantum correlations in a semiconductor microcavity (2002)

Summary form only given. The nonlinear optical response of semiconductor microcavities in the nonperturbative regime has been the subject of many recent experiments. Contrary to clear demonstrations of the quantized nature of the vacuum-field Rabi splitting of a single atom, most of the experiments on semi-conductor microcavities could be explained in terms of a classical light field. Only recently, quantized light field effects have been reported in a coherent control experiment (Lee et al, 1999) and theoretically investigated in secondary emission (Kira et al, 1999). Here, results are presented that display a pronounced third transmission maximum lying energetically between the two normal modes. The third peak can be observed in resonant femtosecond single-beam as well as picosecond pump-probe experiments under various excitation conditions.
Optimizing Losses in Distributed Multiharmonic Matching Networks Applied to the Design of an RF GaN Power Amplifier With Higher Than 80% Power-Added Efficiency (2009)

This paper analyzes the power losses in distributed multiharmonic matching networks and proposes a methodology to minimize these losses, which are critical in designing harmonic controlled or switching mode power amplifiers (PAs). The effect of the harmonic output matching topology on PA performance is studied. An analytical evaluation is developed to show the effect of the harmonic network topology on the conduction losses in the fundamental matching network. This analysis is validated through the comparison of two different matching network topologies in the design of an inverse class F PA with a carrier frequency of around 1 GHz. A 0.2-dB improvement in the losses is achieved, allowing for an improvement of the output power and gain and for an increase in the power-added efficiency by 4%, reaching 81%.
Genetic Control of Radical Crosslinking in a Semi-Synthetic Hydrogel (2019)

Abstract Enhancing materials with the qualities of living systems, including sensing, computation, and adaptation, is an important challenge in designing next-generation technologies. Living materials seek to address this challenge by incorporating live cells as actuating components that control material function. For abiotic materials, this requires new methods that couple genetic and metabolic processes to material properties. Toward this goal, we demonstrate that extracellular electron transfer (EET) from Shewanella oneidensis can be leveraged to control radical crosslinking of a methacrylate-functionalized hyaluronic acid hydrogel. Crosslinking rates and hydrogel mechanics, specifically storage modulus, were dependent on a variety of chemical and biological factors, including S. oneidensis genotype. Bacteria remained viable and metabolically active in the crosslinked network for a least one week, while cell tracking revealed that EET genes also encode control over hydrogel microstructure. Moreover, construction of an inducible gene circuit allowed transcriptional control of storage modulus and crosslinking rate via the tailored expression of a key electron transfer protein, MtrC. Finally, we quantitatively modeled dependence of hydrogel stiffness on steady-state gene expression, and generalized this result by demonstrating the strong relationship between relative gene expression and material properties. This general mechanism for radical crosslinking provides a foundation for programming the form and function of synthetic materials through genetic control over extracellular electron transfer. Significance Statement Next-generation materials will require coupling the advantages of engineered and natural systems to solve complex challenges in energy, health, and the environment. Living cells, such as bacteria, naturally possess many of the qualities essential to addressing these challenges, including sensing, computation, and actuation, using their genetic and metabolic machinery. In addition, bacteria are attractive for incorporation into materials due to their durability, ease-of-use, and programmability. Here, we develop a platform for controlling hydrogel properties (e.g., stiffness, crosslinking rate) using extracellular electron transfer from the bacterium Shewanella oneidensis. In our system, metabolic electron flux from S. oneidensis to a metal catalyst generates radical species that crosslink an acrylate-based macromer to form the gel. This synthetic reaction is under direct control of bacterial genetics and metabolism, which we demonstrate through inducible circuits and quantitative modeling of gene expression and resultant hydrogel properties. Developing methods that capitalize on the programmability of biological systems to control synthetic material properties will enable hybrid material designs with unprecedented functions.
Allophycocyanin B. A common beta subunit in Synechococcus allophycocyanin B (lambda max 670 nm) and allophycocyanin (lambda max 650 nM). (1981)

In cyanobacterial phycobilisomes, light energy absorbed by phycocyanin (lambda max 620 nm) is transferred to allophycocyanin (AP; lambda max 650 nm) and allophycocyanin B (AP-B; lambda max 670 nm) and emitted primarily at 680 nm. This emission maximum coincides with that of pure AP-B. Previous studies have shown that Synechococcus 6301 AP and AP-B are both (alpha beta)3 trimers with a number of similar properties. Here, we show that the beta subunits of AP and AP-B have identical molecular weights, isoelectric points, absorption spectra, NH2-terminal sequences, yield almost indistinguishable tryptic peptide maps, and can substitute for each other in hybridization with the alpha subunits. We conclude that the beta subunits are identical polypeptides. By the same criteria, the alpha subunits of these two proteins are clearly unique polypeptides. The alpha subunits carry the information which determines the absorption and fluorescence emission spectra of the proteins, e.g. the hybrid of the alpha subunits of AP-B with the beta subunits of AP has a lambda max of 670 nm and an emission maximum of 680 nm. In mixtures of AP-B and AP, heterologous trimers are formed in a near-statistical manner by subunit exchange. In such trimers, AP-B alpha beta monomers act as terminal energy acceptors.
Os Calaças: quatro gerações de uma família de cristãos-novos na Inquisição (séculos XVII - XVIII) (2015)

This paper addresses, in an overview, the arrests carried out by the Court of the Holy Office of the Portuguese Inquisition against twelve new Christians belonging to the family lineage of Calaas, charged with observing the Jewish religion. Through the reconstitution of the trajectories of the defendants inserted into this parental trunk, we analyze the inquisitorial persecution against the group from two assumptions: the dismantling of family ties and the varying degrees of Sephardic tradition binding. The historical plot scenarios are the Portuguese city of Elvas, in the mid-17th century, and Rio de Janeiro in the early 18th century, the two occasions when the Calaas are sent to prisons of Tribunal of the Faith, amid the waves of arrests that exceed the family universe. The thesis aims to contribute to the understanding of the ties that bound the new Christians and the limits of strength of these bonds, taking as a starting point the familiar perspective. The inquisitorial sources are privileged, in particular, the lawsuits against Calaas imprisoned, as well as other documents produced in the context of Tribunal of the Faith. However, we also employ primary sources external to the institution, such as coeval critical texts to "cleaning of blood", notarial records and laws, so as to extend the horizon of analytical research.
Preparation of n-type conductive transparent thin films of AgInO2:Sn with delafossite-type structure by pulsed laser deposition (2000)

Sn-doped AgInO2 thin films were prepared on α-Al2O3(0001) single-crystal substrates by pulsed laser deposition. The films prepared under optimized conditions have high optical transmittance up to the near-ultraviolet region and high electrical conductivity. The optical band gap was estimated to be ∼4.1 eV, and electrical conductivity was 7.3×101S cm−1 at 300 K. The carrier concentration and Hall mobility at 300 K were 3.3×1020 cm−3 and 1.4 cm2 V−1s−1, respectively.
Chemical Expansion: Implications for Electrochemical Energy Storage and Conversion Devices (2014)

Many energy-related materials rely on the uptake and release of large quantities of ions, for example, Li + in batteries, H + in hydrogen storage materials, and O 2− in solid-oxide fuel cell and related materials. These compositional changes often result in large volumetric dilation of the material, commonly referred to as chemical expansion. This article reviews the current knowledge of chemical expansion and aspires to facilitate and promote future research in this field by providing a taxonomy for its sources, along with recent atomistic insights of its origin, aided by recent computational modeling and an overview of factors impacting chemical expansion. We discuss the implications of chemical expansion for mechanical stability and functionality in the energy applications above, as well as in other oxide-based systems. The use of chemical expansion as a new means to probe other materials properties, as well as its contribution to recently investigated electromechanical coupling, is also highlighted.
Light scattering from sol-gel Pb(Zr,Ti)O3 thin films: Surface versus volume scattering (1995)

Abstract The optical quality of sol-gel processed Pb(Zr,Ti)O3 thin films has been investigated using spectrally and angularly resolved light scattering. Measurements were performed on a series of films of differing thicknesses, and the results were compared to the predictions of model calculations based upon scattering due to surface roughness, or due to variations of the dielectric constant within the volume of the film. The surface scattering model successfully reproduced many of the features of the observed light scattering. In contrast, the predictions of the volume scattering model differed substantially from the experimental data. In addition, the surface roughness spectrum obtained using atomic force microscopy was used to calculate the angularly resolved light scattering expected for one of the films. For angles greater than ∼20°, the predicted and experimentally determined light scattering were in close agreement. These results indicate that light scattering from these films is primarily due to surface roughness.
Efficient ultraviolet-light (345-nm) generation in a bulk LiIO_3 crystal by frequency doubling of a self-seeded gain-switched AlGaInP Fabry–Perot semiconductor laser (1997)

A self-seeded gain-switched semiconductor laser is applied as a fundamental optical source to second-harmonic generation, and improvement of frequency-conversion efficiency is demonstrated. 345-nm ultraviolet light of 0.12-muW average power is generated in a bulk LiIO(3) crystal for 690-nm fundamental light of 10.5-mW average power, which is composed of 500-MHz pulse trains emitted from an AlGaInP diode laser with a 68-ps temporal width and a 0.11-nm spectral bandwidth. It is clearly shown that the narrowing of the spectral bandwidth by the self-seeding technique gives rise to a normalized conversion efficiency of 0.218%/Wcm , which is fourtimes larger than that for pulses without seeding.
Ex vivo sensing and imaging of corneal scar tissues using terahertz time domain spectroscopy (2021)

Pulsed terahertz (THz) broadband spectroscopy and imaging were applied to investigate ex vivo rabbit corneal scar tissues. Scars with different depths and densities were created by laser ablation on four corneal samples while two corneal samples untouched were used as control. The THz time-domain spectroscopy and reconstructed images illustrated the scar tissue density and gave out depth variation distribution profiles. Calculated absorption coefficient spectra displayed extra absorption peaks compared with control corneas and refractive index spectra showed the optical properties changed at the corneal scar locations. THz spectroscopy and imaging demonstrated adequate contrast in reviewing the scar densities and locations and showed potential applications in depicting spatial distribution and composition changes of corneal scars.