gebhart/patrepeval huggingface dataset:
Coupled-cavity resonant passive mode-locked Ti:sapphire laser (1990)

We use a nonlinear quantum-well reflective sample in a coupled-cavity configuration for resonant passive mode locking of a Ti:sapphire laser, producing tunable pulses as short as 2 psec. Pulses of less than 10-psec duration are observed over a 50-nm wavelength tuning range using a single-quantum-well reflector, over approximately 2 mm of external cavity length detuning. Stable mode-locked pulse trains are obtained without active cavity length control; however, the optical spectrum depends on the phase. We generate up to the sixth harmonic of the fundamental repetition rate, at 1.2 GHz, by simply decreasing the external cavity length.
Ontogeny of 3 beta-hydroxysteroid dehydrogenase/delta 5-delta 4 isomerase (3 beta-HSD) in human testis as studied by immunocytochemistry. (1991)

The enzyme complex 3 beta-hydroxy-5-ene-steroid dehydrogenase/delta 5-delta 4 isomerase (3 beta-HSD) is involved in the biosynthesis of all classes of active steroids, including androgens. To correlate possible changes in 3 beta-HSD with the well-known variations in testosterone secretion during development, the authors localized this enzyme by immunocytochemistry during fetal and postnatal periods of development in the human testis. In the fetal testis, 3 beta-HSD was detected in Leydig cells during the second and third trimester of gestation. In 8-month-old and 11-year-old boys, however, no immunoreaction could be detected in the testis. In pubertal boys, Leydig cells appeared well developed and immunopositive. Since the fluctuations in 3 beta-HSD immunoreactivity are similar to those already observed for androgen secretion, activation of 3 beta-HSD by trophic hormones may play an important role in androgen production during fetal and postnatal development.
Designed Ankyrin Repeat Proteins provide insights into the structure and function of CagI and are potent inhibitors of CagA translocation by the Helicobacter pylori type IV secretion system (2022)

Abstract The bacterial human pathogen Helicobacter pylori produces a type IV secretion system ( cag T4SS) to inject the oncoprotein CagA into gastric cells. The cag T4SS external pilus mediates attachment of the apparatus to the target cell and the delivery of CagA. While the composition of the pilus is unclear, CagI is present at the surface of the bacterium and required for pilus formation. Here, we have investigated the properties of CagI by an integrative structural biology approach. Using Alpha Fold 2 and Small Angle X-ray scattering, it was found that CagI forms elongated dimers mediated by rod-shaped N-terminal domains (CagI N ) and prolonged by globular C-terminal domains (CagI C ). Three Designed Ankyrin Repeat Proteins (DARPins) K2, K5 and K8 selected against CagI interacted with CagI C with subnanomolar affinities. The crystal structures of the CagI:K2 and CagI:K5 complexes were solved and identified the interfaces between the molecules, thereby providing a structural explanation for the difference in affinity between the two binders. Purified CagI and CagI C were found to interact with adenocarcinoma gastric (AGS) cells, induced cell spreading and the interaction was inhibited by K2. The same DARPin inhibited CagA translocation by up to 65% in AGS cells while inhibition levels were 40% and 30% with K8 and K5, respectively. Our study suggests that CagI C plays a key role in cag T4SS-mediated CagA translocation and that DARPins targeting CagI represent potent inhibitors of the cag T4SS, a crucial risk factor for gastric cancer development. Author summary Helicobacter pylori is a bacterial pathogen that colonises the human stomach in half of the world’s population. The most virulent strains use the cag- type IV secretion system ( cag T4SS), a molecular nanomachine capable of injecting the oncoprotein CagA into gastric cells. How CagA is delivered is unknown, but the cag T4SS produces an external appendage referred to as pilus, which interacts with host cell receptors, mediating CagA translocation from the cytoplasm of the bacteria to the inner membrane of the host cell. In this study we have investigated the structural and functional properties of CagI, a protein long-thought to be associated with the cag T4SS pilus but with yet unknown function. We found that CagI displays a unique dimeric structure and that its C-terminal domain is involved in interaction with the host cell. Designed Ankyrin Repeat Proteins were selected against CagI and found to interact with its C-terminal moiety with high affinity. DARPin binding was able to prevent CagI interaction with the host cell and inhibited CagA translocation by H. pylori . Our study reveals the role of CagI in cag T4SS interaction with gastric cells and provides a first example of a small protein binder inhibiting the cag T4SS activity.
TV-constrained incremental algorithms for low-intensity CT image reconstruction (2015)

Low-dose X-ray computed tomography (CT) has garnered much recent interest as it provides a method to lower patient dose and simultaneously reduce scan time. In non-medical applications the possibility of preventing sample damage makes low-dose CT desirable. Reconstruction in low-dose CT poses a significant challenge due to the high level of noise in the data. Here we propose an iterative method for reconstruction which minimizes the transmission Poisson likelihood subject to a total-variation constraint. This formulation accommodates efficient methods of parameter selection because the choice of TV constraint can be guided by an image reconstructed by filtered backprojection (FBP). We apply our algorithm to low-dose synchrotron X-ray CT data from the Advanced Photon Source (APS) at Argonne National Labs (ANL) to demonstrate its potential utility. We find that the algorithm provides a means of edge-preserving regularization with the potential to generate useful images at low iteration number in low-dose CT.
An elliptic low-pass filter with shorted cross-over and broadside-coupled microstrip lines (2003)

An S-band two-layer elliptic type microstrip lowpass filter (LPF) is presented. This filter employs an open-ended cross-over and broadside-coupled microstrip lines with shorting vias to obtain the transmission zeros near the passband. An LPF has been fabricated and measured; simulation and measurement results prove validity of the proposed structure.
Compressed Sensing Off the Grid (2013)

This paper investigates the problem of estimating the frequency components of a mixture of s complex sinusoids from a random subset of n regularly spaced samples. Unlike previous work in compressed sensing, the frequencies are not assumed to lie on a grid, but can assume any values in the normalized frequency domain [0, 1]. An atomic norm minimization approach is proposed to exactly recover the unobserved samples and identify the unknown frequencies, which is then reformulated as an exact semidefinite program. Even with this continuous dictionary, it is shown that O(slog s log n) random samples are sufficient to guarantee exact frequency localization with high probability, provided the frequencies are well separated. Extensive numerical experiments are performed to illustrate the effectiveness of the proposed method.
Graphene Growth via Thermal Decomposition on Cubic SiC(111)/Si(111) (2017)

This chapter discusses the growth of epitaxial graphene on cubic silicon carbide, 3C-SiC(111)/Si(111) and the results obtained by several authors in this research area. Due to the hexagonal structure formed by the cubic (111) face of cubic 3C-SiC, graphene is expected to grow epitaxially. The chapter reviews the details of transformation of SiC to graphene at the atomic level, how graphene growth proceeds with time, and how to produce continuous large areas of graphene on 3C-SiC(111)/ Si(111). The term &quot;epitaxy&quot; comes from Greek, meaning the growth or deposition of a crystalline overlayer on a crystalline substrate. The thermal graphitization of bulk SiC involves heating the sample to temperatures between 1200°C and 1600°C, resulting in the thermal decomposition of the surface. Graphene produced on bulk SiC annealing presents interesting electrical properties. The chapter presents a summary of the knowledge acquired in the recent years regarding graphene growth by Si sublimation on 3C-SiC(111)/ Si(111) in ultrahigh vacuum (UHV).
EFFECT OF CARBON SOURCES AND EXPLANTS ON IN VITRO MULTIPLICATION OF POTATO (2012)

In order to reduce the in vitro production cost, a study was conducted to evaluate the efficacy of two carbon sources viz., sucrose and commercial sugar on in vitro multiplication rate of fifteen potato cultivars using two types of explants. Significant response of carbon sources, explants and cultivars was observed on different morphological characters of in vitro plantlets. Sucrose as a carbon source resulted in a significant increase in the number of nodes in Kufri Badshah, Kufri Chipsona-3, Kufri Giriraj, Kufri Himsona and Kufri Pukhraj which ultimately influences the multiplication rate. However, number of nodes was not affected significantly with the source of carbon in a majority of other potato cultivars viz., Kufri Anand, Kufri Bahar, Kufri Chandramukhi, Kufri Chipsona-1, Kufri Girdhari, Kufri Himalini, Kufri Kanchan, Kufri Lauvkar, Kufri Pushkar and Kufri Sutlej. Use of double node cuttings as explant source resulted in a significant increase in the number of nodes in Kufri Himalini and Kufri Himsona only, whereas, in all other cultivars both the explants viz., double as well as single node performed equally. Thus, in the majority of potato cultivars commercial sugar can be used successfully for reducing the cost of production of in vitro potato plantlets and single node as explants for increasing the multiplication rate without affecting the quality.
Enhanced Convergence and Robust Performance of Randomized Dynamical Decoupling (2006)

We demonstrate the advantages of randomization in coherent quantum dynamical control. For systems which are either time-varying or require decoupling cycles involving a large number of operations, we find that simple randomized protocols offer superior convergence and stability as compared to deterministic counterparts. In addition, we show how randomization may allow us to outperform purely deterministic schemes at long times, including combinatorial and concatenated methods. General criteria for optimally interpolating between deterministic and stochastic design are proposed and illustrated in explicit decoupling scenarios relevant to quantum information storage.
A large-scale investigation of stress response mechanisms in the industrial yeast Kluyveromyces marxianus (2019)

Microbial production strains need to operate under sub- optimal growth conditions such as low pH, high osmolarity and thermal stress. The capacity to carry out industrial fermentations at higher temperatures reduces the risk of bacterial contamination and lowers cooling costs. We want to understand the basis of thermotolerance in the industrial yeast Kluyveromyces marxianus. As part of the EU-funded project, CHASSY, K. marxianus was grown in chemostat cultures under different stress conditions and a multi-omics analysis performed to study a range of stress responses, including elevated temperature (40 °C). Transcriptomes were generated from steady state cultures growing at identical growth rates under different stress conditions and gene set enrichment analysis (GSEA) performed. A range of functions were identified as being specifically expressed at higher temperatures and these are now being further investigated. One example is the temperature-specific expression of two putative hexose transport genes. Subsequent mutational inactivation using CRISPR and heterologous complementation established that at least one of these two genes is required for growth at (40 °C). We are now trying to determine the substrates for, and the precise function of, these genes. We also developed a ribosome profiling pipeline for K. marxianus and are using this to investigate the translational response to temperature stress. The combined study of both transcription and translation at steady state and as a culture responds to a temperature shift will give a comprehensive view of the basis of thermotolerance in K. marxianus and should identify strategies to exploit this in biotechnological processes.
Ultraviolet Photodissociation at 355 nm of Fluorescently Labeled Oligosaccharides (2008)

Ultraviolet photodissociation (UVPD) produces complementary fragmentation to collision-induced dissociation (CID) when implemented for activation of fluorescently labeled oligosaccharide and glycan ions. Reductive amination of oligosaccharides with fluorophore reagents results in efficient photon absorption at 355 nm, producing fragment ions from the nonreducing end that do not contain the appended fluorophore. In contrast to the fragment ions observed upon UVPD (A- and C-type ions), CID produces mainly reducing end fragments retaining the fluorophore (Y-type ions). UVPD affords better isomeric differentiation of both the lacto-N-fucopentaoses series and the lacto-N-difucohexaoses series, but in general, the combination of UVPD and CID offers the most diagnostic elucidation of complex branched oligosaccharides. Four fluorophores yielded similar MS/MS results; however, 6-aminoquinoline (6-AQ), 2-amino-9(10 H)-acridone (AMAC) and 7-aminomethylcoumarin (AMC) afforded more efficient photon absorption and subsequent dissociation than 2-aminobenzamide (2-AB). UVPD also was useful for characterization of glycans released from ribonuclease B and derivatized with 6-AQ. Lastly, electron photodetachment dissociation of oligosaccharides derivatized with 7-amino-1,3-naphthalenedisulfonic acid (AGA) yielded unique cross-ring cleavages similar to those obtained by electron detachment dissociation.
The design and flight test of a 30 kW rocket-borne electron accelerator module (EXCEDE II test). HAES report number 22. Final report, 23 Dec 1974--31 Jul 1975 (1975)

A 30 kW, 3 kV rocket-borne electron accelerator was designed, fabricated, tested and launched from the Poker Flat Research Range as part of the EXCEDE Program. Additional rocket-borne and ground instrumentation provided diagnostic information to evaluate accelerator performance. The high voltage power supply and electron guns were designed specifically for high power deposition. This engineering test demonstrated the accelerator met its design criterion. (GRA)
Robust Surface Detection for Variance Comparison and Dimensional Measurement (2006)

This paper describes a robust method for creating surface models from volume datasets with distorted density values due to artefacts and noise. Application scenario for the presented work is variance comparison and dimensional measurement of homogeneous industrial components in industrial high resolution 3D computed tomography (3D-CT). We propose a pipeline which uses common 3D image processing filters for pre-processing and segmentation of 3D-CT datasets in order to create the surface model. In particular, a pre-filtering step reduces noise and artefacts without blurring edges in the dataset. A watershed filter is applied on the gradient information of the smoothed data to create a binary dataset. Finally the surface model is constructed, using constrained elastic-surface nets to generate a smooth but feature preserving mesh of a binary volume. The major contribution of this paper is the development of the specific processing pipeline for homogeneous industrial components to handle large resolution data of industrial CT scanners. The pipeline is crucial for the following visual inspection of deviations.
The Clinical Significance of Circulating Tumor Cells in the Peripheral Blood (2006)

Tumors launch malignant cells into the circulation continuously. In early stages, the immune surveillance system eliminates these cells from the circulation, but at later times they may persist longer and be detected. The first recorded evidence of the presence of circulating tumor cells in the peripheral blood of cancer patients was documented in 1869. Now, modern molecular biologic and cell sorting techniques make their detection and characterization more practicable. This review will consider the methods currently available for their detection and characterization, and the clinical implications of their presence in various malignant conditions.
Augmenting resolution capabilities of image reconstruction in adaptive electrical capacitance tomography (2016)

In adaptive electrical capacitance tomography (AECT), synthetic electrodes of different sizes are formed by combining the smaller electrode segments. Different sized electrodes can be employed to interrogate different regions of the sensing domain since smaller synthetic electrodes provide higher resolution at the periphery of the domain while larger electrodes are preferred to interrogate the center region of the domain for providing higher signal-to-noise ratio. AECT also enables electronic scanning of (synthetic) electrodes. In this work, we investigate the resolution capabilities of AECT that are achieved by employing electronic scanning and different sized electrodes. Ill-conditioning effects caused by the underdetermined nature of the problem are also investigated by a singular value decomposition analysis of the sensitivity matrix. We also check robustness of reconstruction algorithm against noise.
Cascaded Metasurface Design Using Electromagnetic Inversion With Gradient-Based Optimization (2021)

This article presents an electromagnetic inversion algorithm for the design of cascaded metasurfaces that enables the design process to begin from more practical output field specifications, such as a desired power pattern or far-field (FF) performance criteria. Thus, this method combines the greater field transformation support of multiple metasurfaces with the flexibility of the electromagnetic inverse source framework. To this end, two optimization problems are formed: one associated with the interior space between two metasurfaces and the other for the exterior space. The cost functionals corresponding to each of these two optimization problems are minimized using the nonlinear conjugate gradient (CG) algorithm with analytic expressions for the gradient operators. The numerical implementation of the developed design procedure is presented in detail, including a total variation (TV) regularizer that is incorporated into the optimization procedure to favor smooth field variations from one unit cell to the next. The capabilities of the method are demonstrated by converting the produced surface susceptibilities into three-layer admittance sheet models, which are simulated in several 2-D examples.
A part-transport design and the system for micro-forming applications (2011)

Efforts in micro-forming have been focused largely on fundamental studies and laboratory processes which may ignore some of the key issues related to production realization. A micro-forming machine alone, for example, without a proper handling-system, is seen to be impractical to meet industrial demands. Continuous production requires not just an efficient manufacturing machine, but also autonomous synchronization between the machine and the material-handling system itself. This is inclusive of the way in which the machine automatically transports the finished parts/products away from its working environment and automatically packs the parts/products for shipment. A handling-strategy was presented for the finished parts/products produced by micro-forming, with a focus on the investigation of the handling device and the development of design considerations for a new transportation system for a micro-sheet-forming machine developed at the University of Strathclyde, UK. FE simulation was employed to study the feeding characteristics and also the positional accuracy, and the system was constructed, followed by experimental validations.
Effets comparés de régimes à base de tourteaux de soja ou de colza sur la teneur en histamine de la paroi du tube digestif de rat : rôle de la flore totale (1988)

International audience
Organically Modified Silicates as Inorganic—Organic Polymers (1988)

The combination between inorganic and organic polymeric materials on an atomic scale depends strongly on methods for synthesizing inorganic polymeric networks suitable to the thermal stability of organic materials. The sol-gel process as a "soft-chemistry" method has been proved to be a proper tool for building up inorganic network incorporating organic components. A review over examples for material developments and possibilities of tailoring by chemistry using sol-gel techniques in combination with organic components (organically modified silicates) is given.
High complexity cellular barcoding and clonal tracing reveals stochastic and deterministic parameters of radiation resistance (2020)

Abstract The impact of functional heterogeneity in response to radiation therapy is poorly understood to the present. It remains elusive whether clonal selection of tumor cells in response to ionizing radiation (IR) is a deterministic or stochastic process. We applied high-resolution lentiviral cellular barcoding for quantitative clonal tracking and deconvolution of clonal dynamics in response to IR. Clonal tracking of over 400.000 HNSCC patient-derived tumor cells and the analyses of over 1500 million sequencing reads in clonogenic survival assays reveals that fractionated IR induced a strong selective pressure for clonal reduction. This significantly exceeded uniform clonal survival probabilities indicative for a strong clone-to clone difference within tumor cell lines. IR induced clonal reduction affected the majority of tumor cells ranging between 96-75% and correlated to the degree of radiation sensitivity. Survival and clonogenicity is characterized by an intensive clonal distortion and dominance of individual tumor cells. Survival to IR is driven by a deterministic clonal selection of a smaller population which commonly survives radiation, while increased clonogenic capacity is a result of clonal competition of cells which have been selected stochastically. A 2-fold increase in radiation resistance results in a 4-fold (p&lt;0.05) higher deterministic clonal selection showing that the ratio of these parameters is amenable to radiation sensitivity which correlates to prognostic biomarkers of HNSCC. Evidence for the existence of a rare subpopulation with an intrinsically radiation resistant phenotype commonly surviving IR was found at a frequency of 0.6-3.3% (p&lt;0.001, FDR 3%). With cellular barcoding we introduce a novel functional heterogeneity associated qualitative readout for tracking dynamics of clonogenic survival in response to radiation. This enables the quantification of intrinsically radiation resistant tumor cells from patient samples and reveals the contribution of stochastic and deterministic clonal selection processes in response to IR.