gebhart/patrepeval huggingface dataset:
Validation of a detection scheme based on PCR and isolation for the detection of Xanthomonas axonopodis pv. allii in vegetative parts of Alliaceae and in onion seeds. poster 22 (2016)

Xanthomonas axonopodis pv. allii (Xaa) is the causal agent of bacterial blight of onion (BBO), an emerging disease threatening the world onion production, and causing damage to other Alliaceae, including garlic, welsh onion, shallot, chive and leek. Xaa is an EPPO quarantine organism (A1 list i.e. absent from the EPPO region). The international spread of Xaa can probably be explained by its seedborne status (Roumagnac et al., 2000). Consequently it is of crucial importance to validate efficient detection methods which allow the detection of seedborne pathogens for which the level of inoculum can be very low in very large seed lots. We evaluate a detection scheme based on molecular tests (a triplex quantitative real-time PCR assay (Robène et al., 2015) and a duplex nested end-point PCR assay (Robène-Soustrade et al., 2010)) and isolation. The method assessment was performed following the European standard EN ISO 16140 and the EPPO standard PM7/98 (2). An intra-laboratory study was first conducted, where we characterized the analytical specificity (inclusivity and exclusivity), the analytical sensitivity and the repeatability. We finally tested the detection scheme on naturally contaminated onion seed lots showing different contamination rates. In addition to the intralaboratory study, an inter-laboratory reproducibility trial (including five different laboratories) was performed. This detection scheme was shown to be very efficient, combining a maximal inclusivity (100%), a good exclusivity (83%), a high analytical sensitivity (approximately 103 CFU.mL-1), an excellent repeatability (100% for contamination rates higher than 103 CFU.mL-1) and reproducibility (100% for contamination rates higher than 103 CFU.mL-1). These results allowed to validate the detection scheme as official method of analysis for the French officially approved laboratories (MA 038), and to propose it as an EPPO diagnostic protocol for the detection of this emerging pathogen. (Texte integral)
Accelerated Cardiac Diffusion Tensor Imaging Using Joint Low-Rank and Sparsity Constraints (2017)

Compared to previous methods for accelerating CDTI, the proposed method has the potential to reach higher acceleration while preserving myofiber architecture features, which may allow more spatial coverage, higher spatial resolution, and shorter temporal footprint in the future.
Simplified algorithm of ionizing radiation detecting based on image sensor (2016)

Ionizing particles impacting the photosensing cell of an image sensor induces a current, and event rate statistics can be used to measure the extent of radiation contamination. This paper presents a simple algorithm for detecting ionizing radiation by using the image module of a smartphone. Ionizing radiation exposure experiments revealed that the proposed device has high sensitivity at radiation exceeding 10 μSv/h. Although the CMOS image sensor of a smartphone cannot be used to measure background radiation, it enables the convenient detection of ionizing radiation exceeding 10 μSv/h.
Tritium labeling of detonation nanodiamonds (2014)

The radioactive labeling of detonation nanodiamonds was efficiently achieved using a tritium microwave plasma.
Hyaluronic Acid Derivative with Improved Versatility for Processing and Biological Functionalization (2016)

A hydrophobic/amino functionalized derivative of hyaluronic acid (HA-EDA-C<sub>18</sub> ) has been processed by salt leaching technique as porous scaffold without need of chemical crosslinking. Aim of this work is to demonstrate the improved versatility of HA-EDA-C<sub>18</sub> in terms of processing and biological functionalization. In particular, the chemical procedure to tether thiol bearing RGD peptide has been described. Moreover, the possibility to load and to control the release of slightly water soluble effectors has been demonstrated by using dexamethasone. First, the swelling and degradation profiles of the scaffolds have been investigated, then the evaluation of metabolic activity of bovine chondrocytes, the histological analysis, and microscope observations has been performed to evaluate cellular adhesion and proliferation as well as the production of collagen type II.
Mass spectrometry‐based proteomics: qualitative identification to activity‐based protein profiling (2012)

Mass spectrometry has become the method of choice for proteome characterization, including multicomponent protein complexes (typically tens to hundreds of proteins) and total protein expression (up to tens of thousands of proteins), in biological samples. Qualitative sequence assignment based on MS/MS spectra is relatively well-defined, while statistical metrics for relative quantification have not completely stabilized. Nonetheless, proteomics studies have progressed to the point whereby various gene-, pathway-, or network-oriented computational frameworks may be used to place mass spectrometry data into biological context. Despite this progress, the dynamic range of protein expression remains a significant hurdle, and impedes comprehensive proteome analysis. Methods designed to enrich specific protein classes have emerged as an effective means to characterize enzymes or other catalytically active proteins that are otherwise difficult to detect in typical discovery mode proteomics experiments. Collectively, these approaches will facilitate identification of biomarkers and pathways relevant to diagnosis and treatment of human disease.
A Column-Row-Parallel ASIC Architecture for 3-D Portable Medical Ultrasonic Imaging (2015)

This paper presents a scalable column-row-parallel ASIC architecture for 3-D portable medical ultrasound. Through its programmable row-by-row or column-by-column operations for both transmit and receive beam-formation, linear scaling in interconnection, data acquisition complexity, power dissipation, and programming time is achieved. In addition, its per-element controllers can activate fine granularity aperture definition when more functionality is favored over the linear-scaling power and speed efficiency. This front-end architecture is backward compatible to implement existing widely used array aperture patterns, while supporting new imaging apertures and algorithms. It lends itself very well for the combination with integrated or external digital beamforming circuits. A 16 × 16 proof-of-concept ASIC is fabricated and flip-chip bonded to a 16 × 16 capacitive micromachined ultrasonic transducer (CMUT). Each three-level pulsing transmitter (Tx) is 46% more power efficient than a traditional two-level version, with high-voltage (HV) multiplexers (MUXs) designed for flexible Tx parallelization. Each low-noise receiver (Rx) consumes 1.4 mW active power and 54 μW sleep power, with optimized source follower stages to combine analog outputs for improved SNR. The transceivers are also fault-tolerant to inevitable defects in transducers, greatly enhancing assembly yield. The system demonstrates 3-D plane-wave generation to implement the coherent compounding algorithm for fast volume rate (62.5 volume/s), high-quality 3-D ultrasonic imaging. An interleaved checker board pattern with Iand Q excitations is also demonstrated for ultrasonic harmonic imaging, which reduces transmitted second harmonic distortion (HD2) by over 20 dB.
HDR image noise estimation for denoising tone mapped images (2015)

Tone mapping operators are designed to compress the dynamic range of high dynamic range (HDR) images while preserving the perceived image brightness, but they often enhance image noise in the process, specially in low-light conditions. We propose a method for reducing noise in images created by any tone mapping operator. Our approach leverages the noise distribution of the HDR image to guide the range kernel of a cross bilateral filter that is used to denoise the tone mapped image. When the noise distribution is unknown, we use a new method to automatically estimate it assuming that the HDR image was produced as an average of multiple exposures taken in RAW or JPEG compressed format. Our method performs quantitatively better than existing denoising methods applied on either the original HDR or the tone-mapped images directly, and a user study confirms that it produces visually preferable results.
A method of differential transmission with multiple antennas (2002)

We propose a method for differential transmission with multiple basestation antennas. The method is suitable for mobile cellular applications because it does not require the handset to have more than one antenna or to know the time-varying propagation environment. Yet the method achieves full transmitter diversity and can significantly lower the error probability over a single-antenna system. Some explicit signal constructions are described.
Normal‐dispersion microresonator Kerr frequency combs (2016)

Abstract Optical microresonator‐based Kerr frequency comb generation has developed into a hot research area in the past decade. Microresonator combs are promising for portable applications due to their potential for chip‐level integration and low power consumption. According to the group velocity dispersion of the microresonator employed, research in this field may be classified into two categories: the anomalous dispersion regime and the normal dispersion regime. In this paper, we discuss the physics of Kerr comb generation in the normal dispersion regime and review recent experimental advances. The potential advantages and future directions of normal dispersion combs are also discussed.
H-SCAN+: a practical low-overhead RTL design-for-testability technique for industrial designs (2002)

H-SCAN (1996) was presented as a low overhead design-for-testability strategy which is applicable to RT-level controller-data path circuits. However, from the view-point of practical use, there is a possibility that the area overhead of H-SCAN is larger than that of full-scan. Moreover, H-SCAN is unable to handle many features present in actual designs. In this paper, we propose a modified H-SCAN scheme, called "H-SCAN+", as an improved solution for actual designs. H-SCAN+ consists of several enhancements, including techniques to minimize scan design area overhead, handling of features present in actual designs, and techniques to significantly minimize the running time. We provide comprehensive results of applying H-SCAN+ to several actual RT-level designs.
A synthetic peptide derived from glycine-gated Cl- channel induces transepithelial Cl- and fluid secretion (1997)

M2GlyR is a synthetic 23-amino acid peptide that mimics the second membrane-spanning region of the alpha-subunit of the postsynaptic glycine receptor. This peptide has been shown to form an anion-selective channel in phospholipid bilayers. We have investigated the possibility that the peptide may incorporate into the apical membrane of secretory epithelia and induce the secretion of Cl- and water. We improved the solubility of this peptide by adding four lysine residues to the carboxy terminus, C-K4-M2GlyR, and assayed its channel-forming activity using a subculture of Madin-Darby canine kidney (MDCK) cells. The addition of 100 microM C-K4-M2GlyR to the apical surface of MDCK monolayers significantly increased short-circuit current (Ise), hyperpolarized transepithelial potential difference, and induced fluid secretion. The increase in Ise was inhibited by 100 microM bumetanide and by Cl- channel inhibitors. The effectiveness of the channel blockers followed the sequence niflumic acid > or = 5-nitro-2-(3-phenylpropylamino)benzoate > diphenylamine-2-carboxylate (DPC) > glibenclamide. The effect of the peptide was not inhibited by 4.4'-diisothiocyanostilbene-2-2'-disulfonic acid. Removing Cl from the bathing solutions also inhibited the effect of the peptide. The Cl- efflux pathway induced by C-K4-M2GlyR differs from the native pathway activated by the adenosine 3',5'-cyclic monophosphate (cAMP) agonist, forskolin. First, intracellular cAMP levels were unaffected. Second, the concentration of DPC required to inhibit the effect of the peptide was much lower than that needed to block the forskolin response (100 microM vs. 3 mM). These results support the hypothesis that the synthetic peptide C-K4-M2GlyR can from Cl -selective channels in the apical membrane of secretory epithelial cells and can induce sustained transepithelial secretion of Cl- and fluid.
Mutations in the Hepatocyte Nuclear Factor–1α Gene Are a Common Cause of Maturity-Onset Diabetes of the Young in the U.K. (1997)

Mutations in the hepatocyte nuclear factor-1alpha (HNF1alpha) gene have recently been shown to cause maturity-onset diabetes of the young (MODY). We have examined 15 U.K. MODY families for mutations in the coding region of the HNF-1alpha gene. Eight different mutations, three frameshift (P291fsinsC, P379fsdelCT, and A443fsdelCA) and five missense mutations (P129T, R131W, R159W, P519L, and T620I), were identified in eleven families (73%). The previously reported mutation P291fsinsC was found in four pedigrees. A screen of a further 32 probands with early onset (<40 years of age) NIDDM showed the mutation in two additional families. This common mutation was present on at least three different haplotypes, suggesting that its high frequency is due to recurrent mutation rather than a founder effect. We have demonstrated that mutations in the HNF-1alpha gene are a common cause of MODY in U.K. families and result in early onset NIDDM with a progressive clinical course. Mutation-based genetic counseling can now be considered for the majority of patients with MODY.
Alcoholic hepatitis: Challenges in diagnosis and management (2015)

Alcoholic hepatitis, in its severe form, is a devastating acute condition that requires early recognition and specialized tertiary medical care. This paper summarizes its epidemiology, pathophysiology, assessment, and treatment.
Expression and factor-dependent modulation of the interleukin-3 receptor subunits on human hematopoietic cells (1993)

Interleukin-3 (IL-3) regulates growth and differentiation of multipotential as well as lineage-committed progenitor cells. The human IL-3 receptor (IL-3R) consists of the alpha and common beta (beta c) subunits. The alpha subunit (IL-3R alpha) is specific for IL-3 and binds IL-3 with low affinity. In contrast, the beta c subunit does not bind any cytokine by itself, but forms a high-affinity receptor with IL- 3R alpha. As the same beta c subunit also forms high-affinity receptors for IL-5 and granulocyte-macrophage colony-stimulating factor (GM-CSF) with the respective cytokine-specific alpha subunit, the expression of the alpha subunits is responsible for specificity of cytokines. To examine the expression of IL-3R alpha, we have developed a monoclonal antibody (MoAb), N3A. N3A specifically bound to cells expressing IL-3R alpha and immunoprecipitated a 75 Kd glycoprotein, which became 43 Kd on N-glycosidase digestion. N3A and an anti-beta c antibody, CRS1, were used in double color fluorescence-activated cell sorter (FACS) staining with several lineage markers to see the IL-3R expression pattern in peripheral blood (PB), cord blood (CB), and bone marrow (BM) cells. Both IL-3R subunits were expressed on myeloid cell lineages (CD13+, CD14+, CD15Lo, or CD33+). To further study the IL-3R expression on hematopoietic progenitor cells, the CD34+ populations were isolated from both BM and CB cells. Those populations showed positive staining profiles with the N3A MoAb and were weakly stained with the CRS1 MoAb. Furthermore, anti c-kit antibody staining of the CD34+ fraction from CB, but not from BM, showed two intensities and the IL-3R alpha expression seemed to be higher in a fraction of low c-kit expression. Because IL-1, IL-6, G-CSF, stem cell factor (SCF), interferon (IFN)- gamma, and tumor necrosis factor (TNF)-alpha are known to enhance IL-3- dependent colony formation, we have examined whether this enhancement could be correlated with upregulation of the IL-3R expression. Incubation of CD34+ cells with TNF-alpha for 2 days significantly increased the level of beta c and G-CSF increased the number of cells with high level expression of alpha, while other factors did not affect the IL-3R expression. Thus, different cytokines appear to have different mechanisms for enhancement of IL-3-dependent proliferation.
Faithful expression of living color reporter genes in transgenic medaka under two tissue‐specific zebrafish promoters (2005)

To test tissue specificity of zebrafish gene promoters in a heterologous fish species, two transgenic medaka lines under two zebrafish promoters were generated. Under the zebrafish skeletal muscle-specific mylz2 promoter, transgenic medaka expressed green fluorescent protein (GFP) exclusively in skeletal muscles, mimicking the endogenous medaka mylz2 mRNA expression and also identical to GFP expression in mylz2:gfp transgenic zebrafish. A madaka mylz2 promoter was also capable of directing skeletal muscle-specific GFP expression in transient transgenic zebrafish embryos. In the krt8:rfp transgenic medaka line with the zebrafish epithelial krt8 promoter, red fluorescent protein was specifically expressed in the skin epithelia as well as the epithelial lining cells of the anterior digestive tract, which was also identical to GFP expression in krt8:gfp transgenic zebrafish. Therefore, the two zebrafish promoters faithfully function in a heterologous fish species, and it is likely that the mechanisms of tissue-specific expression are largely conserved among fish species.
AUTOMATIC PHONETIC BASEFORM DETERMINATION s3.5 (1991)

Plionet,ic haseforms are the basic recognition units in rim! large vocabulary speech recognition systems Tlirsr I,asrhrlns we usitally determined by hand once a vocabulary is clinswi and no1 modified thereafter. However, many applical,ions nf speech recognit ion, such as dictatioil transcription, arp hampered by a fixed vocabulary and require flic user be aldr lo add nen words to the vocahulary At least ono plionrl,ir IGWform must he assigned to each new word to properly inlcgralc the wsord into the recognition system. Dictionary lookup IS nften ~~nsuccessful in determining n phonetic baselorin Iwcaliw new words are often names or task-specific jargon; also, talkers tend to have idiosyncratic pronunciations lor a suhslanlinl fraction ol wokds. This paper describes a series of experiineiil.c in which the phonetic baselorm is deduced autoinalically lor new words by utilizing actual utterances of the new wnrd iii conjunction with a set ol automatically derived spelling-losound rules. We evaluated recognition perlorinance on iien words spoken by two different talkers when the phonetic liasrforms were extracted via the above approach Thr error ralps on these new words were found to be comparable to or Iwtlvr than when t,lie phonetic baseforins were dcriveil I)? Iiaiiil. 111115 validat,ing the basic approach
Nanoscale coherent light sources on GaAs and Si using single rolled-up InGaAs/GaAs quantum dot microtubes (2009)

In this report we study the nanoscale coherent light sources on GaAs and Si using single rolled-up InGaAs/GaAs quantum dot microtubes. Such microtubes are formed by self-rolling of coherently strained InGaAs/GaAs quantum dot heterostructures through controlled release from their host substrates [1-3]. We have developed a substrate-on-substrate transfer process [3] and realized nearly defect-free quantum dot microtubes on Si that were not possible before. Emission characteristics of InGaAs/GaAs quantum microtubes were studied using micro-photoluminescence spectroscopy at 300 K. A typical emission spectrum measured from the freestanding region of a microtube without any intentional surface corrugations (inset) is shown in Fig. 3(a) (solid line), which is characterized by a sequence of regularly spaced optical resonance modes superimposed on a broad quantum dot emission spectrum (dotted line). These resonance modes arise from photons circulated around the periphery of the microtube by total internal reflections.
Multiple-input optical control of vertical cavity surface emitting lasers using intracavity-coupled in-plane lasers (1996)

We report new experimental results demonstrating optical bistability and two-input NOR gate operation in intracavity-coupled in-plane and vertical cavity surface emitting lasers (VCSELs) fabricated from the same epitaxial material. The VCSEL (or output) section gain is controlled by separately biased in-plane laser section(s), and depending on the in-plane power output, complete quenching of stimulated emission in the VCSEL is observed. Hysteresis is present in the VCSEL output power versus in-plane laser input power characteristic, and an optical memory effect is observed in the combined device.
An Unbiased Proteomics Method to Assess the Maturation of Human Pluripotent Stem Cell–Derived Cardiomyocytes (2019)

We established an unbiased proteomics method that can provide accurate and specific assessment of the maturity of hPSC-cardiomyocytes and identified new markers of maturation. Furthermore, this integrated proteomics strategy laid a strong foundation for uncovering the molecular pathways involved in cardiac development and disease using hPSC-cardiomyocytes.
Conceptual modeling of data-intensive Web applications (2002)

Many of the Web applications around us are data-intensive; their main purpose is to present a large amount of data to their users. Most online trading and e-commerce sites fall into this category, as do digital libraries and institutional sites describing private and public organizations. Several commercial Web development systems aid rapid creation of data-intensive applications by supporting semiautomatic data resource publishing. Automatic publishing is typically subject to the constraints of database schemas, which limit an application designer's choices. Thus, Web application development often requires adaptation through programming, and programs end up intricately mixing data, navigation, and presentation semantics. Presentation is often a facade for elements of structure, composition, and navigation. Despite this frequently unstructured development process, data-intensive applications, based on large data sets organized within a repository or database, generally follow some typical patterns and rules. We describe these patterns and rules using WebML as a conceptual tool to make such notions explicit. WebML is a conceptual Web modeling language that uses the entity-relationship (ER) model for describing data structures and an original, high-level notation for representing Web content composition and navigation in hypertext form.