gebhart/patrepeval huggingface dataset:
The flowering hormone florigen accelerates secondary cell wall biogenesis to harmonize vascular maturation with reproductive development (2019)

Florigen, a proteinaceous hormone, functions as a universal long-range promoter of flowering and concurrently as a generic growth-attenuating hormone across leaf and stem meristems. In flowering plants, the transition from the vegetative phase to the reproductive phase entails the orchestration of new growth coordinates and a global redistribution of resources, signals, and mechanical loads among organs. However, the ultimate cellular processes governing the adaptation of the shoot system to reproduction remain unknown. We hypothesized that if the mechanism for floral induction is universal, then the cellular metabolic mechanisms underlying the conditioning of the shoot system for reproduction would also be universal and may be best regulated by florigen itself. To understand the cellular basis for the vegetative functions of florigen, we explored the radial expansion of tomato stems. RNA-Seq and complementary genetic and histological studies revealed that florigen of endogenous, mobile, or induced origins accelerates the transcription network navigating secondary cell wall biogenesis as a unit, promoting vascular maturation and thereby adapting the shoot system to the developmental needs of the ensuing reproductive phase it had originally set into motion. We then demonstrated that a remarkably stable and broadly distributed florigen promotes <i>MADS</i> and <i>MIF</i> genes, which in turn regulate the rate of vascular maturation and radial expansion of stems irrespective of flowering or florigen level. The dual acceleration of flowering and vascular maturation by florigen provides a paradigm for coordinated regulation of independent global developmental programs.
A rapid, low‐dose, 13C‐urea tablet for the detection of Helicobacter pylori infection before and after treatment (2003)

New 10-min 13C-UBTs using tablet formulations of 13C-urea with citric acid are reliable for the assessment of H. pylori status pre- and post-treatment.
Vacant technology forecasting using new Bayesian patent clustering (2013)

Vacant technology forecasting (VTF) is a technology forecasting approach to find technological needs for given industrial field in the future. It is important to know the future trend of developing technology for the R&D planning of a company and a country. In this paper, we propose a new Bayesian model for patent clustering. This is a VTF methodology based on patent data analysis. Our method is composed of Bayesian learning and ensemble method to construct the VTF model. To illustrate the practical way of the proposed methodology, we perform a case study of given technology domain using retrieved patent documents from patent databases in the world.
Is water saturation a fracability indicator for organic‐rich, yet low‐clay content, tight carbonate source rock reservoirs? (2021)

Abstract Hydraulically fracturing long horizontal wells is the key technology for economically producing hydrocarbon from unconventional reservoirs. A reservoir's fracability (the ease by which it can be hydraulically fractured) has often been used as an important parameter for identifying the sweet spots for production. Several fracability indicators, based on different types of rock properties, including mechanical, geochemical, and mineralogical properties, have been developed and used in industry. This study, based on observations from a source rock reservoir, proposes the use of reservoir water saturation as a new fracability indicator for organic‐rich tight carbonate source rocks that are not clay rich. The results from a machine learning model trained with the observations clearly show the strong and positive correlation between the linear flow parameter (that is obtained based on the newly proposed equivalent‐state approximation and characterizes the effectiveness of hydraulic fracturing) and the water saturation for oil wells, but not for gas wells. While further investigation is needed, the results may be due to the dual wettability of the carbonate source rock. Since minerals are more water‐wet than the organic matter, reservoir water tends to occupy pore spaces in the mineral matrix. Thus, water saturation reflects the relative portion of mineral matrix pore spaces. Given that the low‐clay content mineral matrix contains all the brittle components, the pore‐space development in the mineral matrix may have important implications for the fracability in the hydraulic fracturing process.
Structural and Evolutionary Relationships among Protein Tyrosine Phosphatase Domains (2001)

Udgivelsesdato: 2001-Nov
Constitutive Gene Expression Predisposes Morphogen-Mediated Cell Fate Responses of NT2/D1 and 27X-1 Human Embryonal Carcinoma Cells (2006)

Human embryonal carcinoma (EC) cell lines exhibit considerable heterogeneity in their levels of pluripotency. Thus, NT2/D1 cells differentiate into neural lineages upon exposure to all-trans retinoic acid (ATRA) and non-neural epithelial lineages upon exposure to bone morphogenetic protein-2 (BMP-2). In contrast, 27X-1 cells differentiate into extra-embryonic endodermal (ExE) cells upon treatment with either morphogen. To understand the molecular basis for the differential responses of the two cell lines, we performed gene expression profiling at the undifferentiated EC cell line state to identify constitutive differences in gene expression. NT2/D1 cells preferentially expressed transcripts associated with neurectodermal development, whereas 27X-1 cells expressed high levels of transcripts associated with mesendodermal characteristics. We then determined temporal expression profiles of 27X-1 cells during ExE differentiation upon treatment with ATRA and BMP-2 and compared the data with changes in gene expression observed during BMP-2- and ATRA-induced differentiation of NT2/D1 cells. ATRA and BMP-2 induced distinct sets of transcription factors and phenotypic markers in the two EC cell lines, underlying distinct lineage choices. Although 27X-1 differentiation yielded comprehensive gene expression profiles of parietal endodermal lineages, we were able to use the combined analysis of 27X-1 data with data derived from yolk sac tumors for the identification of transcripts associated with visceral endoderm formation. Our results demonstrate constitutive differences in the levels of pluripotency between NT2/D1 and 27X-1 cells that correlate with lineage potential. This study also demonstrates that EC cells can serve as robust models to investigate early lineage choices during both embryonic and extra-embryonic human development.
A novel design for deadzone-less fast charge pump with low harmonic content at the output (2004)

A novel design for a charge pump is presented. Unlike common charge pumps where the transistors are operating as switches, in this design transistors are kept in their saturation region at all times. This design has resulted in faster operation of the pump in addition to lower levels of output harmonic content. The actual strong point of this design is the smooth change of the output current. This may result in small spurious and phase noise levels if this charge pump is used in a PLL or frequency synthesizer. Comparison of simulation results for this circuit and those of a regular charge pump reveals the potential superiority or this design over traditional circuits.
The global state of clinical research and trends in periprosthetic joint infection: A bibliometric analysis (2020)

Based on the current trends of globalization, there is a rising trend in publications on PJI, with the largest annual contributions made by the United States. The most influential contributors are researchers from the United States and Europe. Twitter is used as a platform to communicate knowledge by most PJI researchers. The most recent research has focused on the diagnosis and risk factors of PJI.
Toward Immersed Boundary Simulation of High Reynolds Number Flows (2003)

The fraction of fibers coated in a total of 3,800 asbestos fibers from 38 patients with disease related to asbestos (100 fibers per patient) was determined, according to asbestos fiber type and size parameters. Among the 3,800 fibers, 638 (16.8%) were coated and 3,162 were uncoated. All fibers were analyzed at 2,000 x magnification (lower limit of detection: 2 microns for length and 0.06 microns for diameter). The diameter of the totally coated fibers (28.4% of total bodies; 181/638) was not measured. The percentage of coated fibers varied with the asbestos type; it was 27.1% (335/1235) for amosite fibers, 16.0% (228/1423) for crocidolite, 6.6% (60/908) for tremolite or actinolite, 6.5% (14/214) for anthophyllite, and 5% (1/20) for chrysotile fibers. Most coated fibers were longer than 10 microns and had an aspect ratio (length/diameter) of more than 20. Approximately 60% of coated fibers had an aspect ratio of more than 100. The longer the fiber, the greater the percentage of coated fibers, regardless of diameter. The increase in the percentage associated with length was more marked in fibers with a smaller diameter; the percentage of coated fibers was, therefore, greater in fibers 30 microns or less in diameter. However, in fibers longer than 30 microns, the relationship to percentage of coated fibers was not as clear, and the diameter was less important. Accordingly, the fibers with high aspect ratios, particularly long fibers, tended to show asbestos body formation. The percentage of long fibers was highest in amosite, and the percentage of fibers with an aspect ratio of more than 100 was highest in amosite and crocidolite.(ABSTRACT TRUNCATED AT 250 WORDS)
Angular accuracy of a phased array radar (1961)

One type of phased-array radar of current interest employs an array of separate receiving elements, each followed by an individual amplifier. These individual signals are combined coherently to form one or more receiving beams for searching, tracking, or performing both functions simultaneously. This paper presents an approach to the theory of angle measurement with a phased array of this type. In the one-dimensional problem considered here, the receiving antenna consists of a linear array of individual antenna-amplifier elements. The receiver-noise-limited case is considered, in which accuracy is limited by the additive normally distributed noise present in each channel. An expression is derived for the limiting accuracy of angular measurement when a single set of samples is available. This set of samples is obtained simultaneously, one sample from each channel. Next, two methods of implementing the angular measurements are discussed. These are amplitude comparison monopulse and a coherent or phase comparison technique. For large signal-to-noise ratios and for either a square law or a linear envelope detector, the accuracy of amplitude comparison monopulse approaches the theoretical limit. The same accuracy can be achieved with the coherent technique by proper weighting of the individual signals.
Efficacy and safety of peanut epicutaneous immunotherapy in patients with atopic comorbidities (2022)

The results support the safety and efficacy of VP250 for treating peanut-allergic children with or without concomitant atopic conditions.
Partial response class I signaling applied to high density magnetic recording (2002)

For high density magnetic recording systems, equalizing to partial response signals of the form (1-D)(1+D)/sup n/ and applying modulation codes with spectral nulls at DC and the Nyquist frequency have been proposed in Karabed and Siegel (1991). The present authors consider using the same DC/Nyquist-free codes, but equalizing to class I partial response signals with polynomial, (1+D). They find that when the received signal is detected by a Viterbi detector based upon a trellis that combines the equalized channel with the modulation constraint, the simpler detector for class I performs comparably to class IV, (1-D/sup 2/), or extended class IV (1+D-D/sup 2/-D/sup 3/) detectors.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Generation of hepatocytes and pancreatic endocrine cells from human induced endodermal progenitor like cells (2015)

Rangarajan Sambathkumar, Philip Roelandt1, Manoj Kumar1, Ana Rita Mestre Rosa1, Fanos Tadessa Woldemariyam1, Renate Akkerman1, Sumitava Dastidar2, Qing Cai1, Eric Kalo1, Valerie Roobrouck3, Satish Khurana1, Marijke Faas5, Paul de Vos5, Catherine M Verfaillie1. New sources of cells are needed for both therapy of diabetes (beta cells) and creation of hepatocytes (for toxicology and metabolization studies). One possibility are induced pluripotent stem cells generated from fibroblasts and then differentiated towards the lineage of interest. One drawback, definitely for clinical therapies is the possible persistence of pluripotent cells that might form teratomas. An alternative approach is to de-differentiate somatic cells to an intermediate progenitor, such as endodermal progenitors, which can then be committed to beta-cells and / or hepatocytes. We previously reported that using 16 TFs, human multipotent adult progenitor cells (MAPCs) could be transdifferentiated in cells with epithelial morphology, that could be expanded long term and expressed (mes)endodermal genes. However, more mature endodermal genes were also expressed including Albumin (ALB). We therefore tested a combination of 14 TF, which now resulted in iENDO cells; expandable cells with (mes)endodermal endogenous gene expression but without mature endodermal gene expression. Using adapted protocols for pancreatic endocrine cell differentiation and hepatocyte differentiation, we demonstrated that 14 TF iEndo cells could be committed to endocrine pancreatic endoderm, expressing PDX1, NGN3, PAX4, NKX2.2, NEUROD1, MAFA and MAFB, but not mature beta cell characteristics (no Insulin expressed). During hepatocyte differentiation, hepatoblast genes such as AFP, ALB, AAT were induced. Inability to create fully committed progenitors at this point may be because the differentiation conditions are not yet fully optimized. A second possibility is that the OCT4 transgene used in the preprogramming remains expressed. Currently we are testing if doxycycline inducible overexpression of OKSM combined with the other 10 TFs may support full differentiation towards beta cells and hepatocytes. Preliminary results suggest that upon transplantation of undifferentiated 14TFs iENDO cells under the kidney capsule of SCID mice, cells are differentiating to the hepatocyte lineage In vivo. Studies wherein iENDO cells differentiated to endocrine pancreatic cells are evaluated following grafting in vivo are pending.
On some time-frequency signatures in stereo-electroencephalography (SEEG) (2002)

This paper is aimed at depicting particular features observed in SEEG seizures by means of time-frequency (TF) analysis. The identification of these signatures, from simple to complex, anatomically referenced, represent a first step towards: (i) a better understanding of the underlying mechanisms and (ii) more efficient data-oriented signal processing methods.
Effects of Word-frequency based Pre- and Post- Processings for Audio Captioning (2020)

The system we used for Task 6 (Automated Audio Captioning)of the Detection and Classification of Acoustic Scenes and Events(DCASE) 2020 Challenge combines three elements, namely, dataaugmentation, multi-task learning, and post-processing, for audiocaptioning. The system received the highest evaluation scores, butwhich of the individual elements most fully contributed to its perfor-mance has not yet been clarified. Here, to asses their contributions,we first conducted an element-wise ablation study on our systemto estimate to what extent each element is effective. We then con-ducted a detailed module-wise ablation study to further clarify thekey processing modules for improving accuracy. The results showthat data augmentation and post-processing significantly improvethe score in our system. In particular, mix-up data augmentationand beam search in post-processing improve SPIDEr by 0.8 and 1.6points, respectively.
Thermoelectric Power Conversion using Generation of Electron-Hole Pairs in Large Area p-n Junctions (2006)

A new method for thermoelectric power generation using large area pn-junctions is presented [Span, et al., 2005]. Normally, thermal generation of electron-hole pairs is avoided because of the deteriorating effects of the minority carriers on the efficiency in classical thermocouples. A temperature gradient applied along the pn-junction causes a flux of carriers from hot to cold due to the Seebeck effect, which introduces a reverse bias and thus thermal generation in the hot part of the pn-structure. The generation of electron-hole pairs leads to a multitude of new properties that can be used to enhance the efficiency of the energy conversion. The generation rate of electron-hole pairs is a highly adjustable parameter, which makes it possible to tailor thermoelectric elements and modules to given boundary conditions. This is achieved by changing the amount and distribution of generation centers and the shape of the temperature gradient as well as the choice of the material system. Due to the generation of electrons and holes, no contact on the hot side of the thermoelectric element is necessary. Limitations of the hot side temperature caused by mechanical stress due to different thermal expansion of different materials or by the solder or joining material are therefore non-existing. To describe these structures, an effective figure of merit Z <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">eff</sub> is calculated using the device simulator Minimos-NT [2004]
Optical decoherence and energy level structure of 0.1%Tm3+:LiNbO3 (2012)

We report the energy level structure of the ${}^{3}$H${}_{6}$ and ${}^{3}$H${}_{4}$ multiplets for Tm${}^{3+}$ doped congruent LiNbO${}_{3}$, as well as the decoherence properties and their temperature dependencies for the ${}^{3}$H${}_{6}(1){\ensuremath{\leftrightarrow}}^{3}$H${}_{4}(1a)$ transition at 794 nm. It is shown that this material provides very significant improvements in bandwidth, time-bandwidth product, and sensitivity for spatial-spectral holographic signal processing devices and quantum memories based on spectral hole burning. The available signal processing bandwidth for 0.1$%$Tm${}^{3+}$:LiNbO${}_{3}$ is 300 GHz versus 20 GHz for Tm${}^{3+}$YAG. The peak absorption coefficient for 0.1$%$Tm${}^{3+}$:LiNbO${}_{3}$ is 15 cm${}^{\ensuremath{-}1}$ at 794.5 nm compared with 1.7 cm${}^{\ensuremath{-}1}$ for 0.1$%$Tm:YAG at 793 nm, and the total absorption strength is eighty times stronger. The oscillator strength for Tm${}^{3+}$:LiNbO${}_{3}$ is about twenty-five times larger than that for Tm${}^{3+}$:YAG, making the material five times more sensitive for processing high-bandwidth analog signals. The homogeneous linewidth, which determines processing time or spectrum analyzer resolution, is 30 kHz at 1.6 K and 350 kHz at 6 K, as measured by photon echoes. Those values establish potential time-bandwidth products of 10${}^{7}$ and 7 $\ifmmode\times\else\texttimes\fi{}$10${}^{5}$, respectively. The temperature dependence of the homogeneous linewidth was explained by observation of a 7.8 cm${}^{\ensuremath{-}1}$ crystal field level in the ground multiplet and direct phonon coupling. The excited state ${}^{3}$H${}_{4}$ lifetime ${T}_{1}$ is 152 $\ensuremath{\mu}$s and the bottleneck lifetime of the lowest ${}^{3}$F${}_{4}$ level is 7 ms from photon echo measurements. These factors combine to provide a surprisingly large increase in key parameters that determine material performance for spatial-spectral holography, quantum information, and other spectral hole burning applications.
Prototype Atomic Force Microscope System with Micro-four-point Probe for Quantitative Characterization of Local Electrical Conductivity (2009)

An atomic force microscope probe for local conductivity measurement is presented.The minimum space of the four-point atomic force microscope(AFM) probe is 300 nm.The AFM system with the newly developed four-point probe not only inherits the function of AFM surface topography generating but also has the capability of characterizing the local conductivity simultaneously.The local conductivities of aluminum and indium tin oxide thin films of 6.0 μm and 350 nm thick are quantitatively measured respectively.The conductivity measurements indicate this four-point AFM probe technique has the capability of measuring submicrometer electrical conductivity.
Engineering Bifidobacterium longum Endo-α-N-acetylgalactosaminidase for Neu5Acα2-3Galβ1-3GalNAc reactivity on Fetuin (2022)

Endo-α-N-acetylgalactosaminidase from Bifidobacterium longum (EngBF) belongs to the glycoside hydrolase family GH101 and has a strict preference towards the mucin type glycan, Galβ1-3GalNAc, which is O-linked to serine or threonine residues on glycopeptides and -proteins. While other enzymes of the GH101 family exhibit a wider substrate spectrum, no GH101 member has until recently been reported to process the α2-3 sialidated mucin glycan, Neu5Acα2-3Galβ1-3GalNAc. However, work published by others (ACS Chem Biol 2021, 16, 2004-2015) during the preparation of the present manuscript demonstrated that the enzymes from several bacteria are able to hydrolyze this glycan from the fluorophore, methylumbelliferyl. Based on molecular docking using the EngBF homolog, EngSP from Streptococcus pneumoniae, substitution of active site amino acid residues with the potential to allow for accommodation of Neu5Acα2-3Galβ1-3GalNAc were identified. Based on this analysis, the mutant EngBF variants W750A, Q894A, K1199A, E1294A and D1295A were prepared and tested, for activity towards the Neu5Acα2-3Galβ1-3GalNAc O-linked glycan present on bovine fetuin. Among the mutant EngBF variants listed above, only E1294A was shown to release Neu5Acα2-3Galβ1-3GalNAc from fetuin, which subsequently was also demonstrated for the substitutions: E1294 M, E1294H and E1294K. In addition, the k<sub>cat</sub>/K<sub>M</sub> of the EngBF variants for cleavage of the Neu5Acα2-3Galβ1-3GalNAc glycan increased between 5 and 70 times from pH 4.5 to pH 6.0.
Experimental analysis of process induced draping effects in textile preforms (2019)

The local mechanical properties of fiber reinforced composites strongly depend on the local fiber orientation which is created during preforming. To date, investigations on fiber orientation effects focus on the analysis of the overall structure and on a qualitative description of local effects because it is still difficult to quantify local draping effects. This paper presents a tooling concept which allows influencing the preforming of the fabric and thus an approach to quantify local draping effects. Based on the optical inspection system Atos, the size of different draping effects are measured and classified for NCF-reinforced CFRP composites.