gebhart/patrepeval huggingface dataset:
Action of Plant Growth Regulators. III. Adsorption of Aromatic Acids to Oat Monolayers (1960)

In an earlier paper (2) it was concluded that a broad correlation exists between the resistance of a plant to 2-methyl-4-chlorophenoxyacetic acid (MCPA) and its ability to adsorb the growth regulator. This lent support to the suggestion that the foundation of species resistance may be partly based on the extent of MCPA adsorption to sites not concerned in the physiological response. This work has been extended since it follows that the biological activity of different growth regulator molecules on a given plant species may also be limited by the extent of their adsorption, and a correlation may exist between biological activity and the adsorption of growth regulators to plant constituents. This has already been implied by Veldstra and Booij (9) when noting that chlorination of the phenoxy compounds generally appeared to increase their activity but chlorination of naphthoxy compounds reduced their activity. Similarly, these authors consider that certain trichlorophenoxy acetic acids have exceeded the optimum size and hence optimum interaction with plant membranes, for high biological activity. Three series of acids were investigated. The phenoxyacetic and benzoic acids were selected in view of the importance of some members of these series as herbicides. The phenylacetic acids were studied as a result of earlier observations at Jealott's Hill in 1953 that 2,3-dichloro and 2,6-dichlorophenylacetic acids were compounds with biological activity similar in character but somewhat inferior to MCPA. This paper presents physical measurements of the adsorption of the acids to monolayers from the squashes prepared from oat leaves using the Langmuir trough. No biological data are presented in this paper but it is hoped it will be possible to seek a correlation when the results of biological tests on phenylacetic acids being made by various research teams become available. It is proposed to present these in Part IV of this series. MATERIALS AND METHODS
Ultrasound Imaging of Apoptosis: DNA-Damage Effects Visualized (2003)

This chapter presents a new method for the detection of DNA damage that leads to the physiological process of apoptosis which is a normal programmed cell-death response to sufficiently toxic levels of DNA damage. The high-frequency ultrasonic detection of programmed cell death has been demonstrated in vitro, in situ, and in vivo using a variety of different apoptosis inducing methods (1,2). This method provides a useful image based adjunct for the detection of programmed cell death in a laboratory setting as well as being a powerful potential clinical tool which can be used to monitor tumour responses to treatment. Typical low-frequency medical ultrasound imaging devices operate at 1–10 MHz, provide mainly low resolution structural information, and predominantly are used in obstetrics and cardiology. In contrast, high-frequency ultrasound imaging devices operate at 30–50 MHz and offer increased resolution as well as the emerging capability to detect cells and tissues in different physiological states including those undergoing programmed cell death, or apoptosis (1–4). Data collected to date indicates that this capability of high-frequency ultrasound is based on interactions of high-frequency ultrasound waves with the chromosomal nuclear material in cells, which undergoes structural changes of condensation and subsequent fragmentation with the process of programmed cell death (1–2,4). We have demonstrated this process experimentally in vitro, in situ, and in vivo using a number of different systems in which apoptosis is induced with physiological stimuli, chemotherapeutic drugs, radiation, or photodynamic therapy. The ultrasound-based approach to detecting apoptosis has a number of potential applications which range from embryological studies of development where apoptosis plays an important role, to assessing organ viability for the purposes of transplantation, again a situation where the presence of programmed cell death is correlated to clinical outcome (5).
The novel chemokine engineered stromal cell derived factor-1alpha recruits endothelial progenitor cells to the infarct borderzone; results from an egfp+ bone marrow chimera model (2013)

METHODS: 103 patients with degenerative mitral regurgitation (MR) underwent single-suture repair of the mitral valve through a 3-cm right chest incision from May 2007 through December 2012. The prolapsed segment of the mitral valve was imbricated with a double running CV 5 Gore-Tex suture, resulting in a smooth plane of coaptation. Preoperative and perioperative echocardiograms as well as patient outcomes were analyzed and compared to patients undergoing minimally invasive isolated mitral valve repair using quadrangular resection at the same institution during the same time period.
Novel image classification based on integration of EEG and visual features via MSLPCCA (2015)

This paper presents a novel image classification method based on integration of EEG and visual features. In the proposed method, we obtain classification results by separately using EEG and visual features. Furthermore, we merge the above classification results based on a kernelized version of Supervised learning from multiple experts and obtain the final classification result. In order to generate feature vectors used for the final image classification, we apply Multiset supervised locality preserving canonical correlation analysis (MSLPCCA), which is newly derived in the proposed method, to EEG and visual features. Our method realizes successful multimodal classification of images by the object categories that they contain based on MSLPCCA-based feature integration.
Non-invasive mouthguard biosensor for continuous salivary monitoring of metabolites (2014)

The present work describes the first example of a wearable salivary metabolite biosensor based on the integration of a printable enzymatic electrode on a mouthguard. The new mouthguard enzymatic biosensor, based on an immobilized lactate oxidase and a low potential detection of the peroxide product, exhibits high sensitivity, selectivity and stability using whole human saliva samples. Such non-invasive mouthguard metabolite biosensors could tender useful real-time information regarding a wearer's health, performance and stress level, and thus hold considerable promise for diverse biomedical and fitness applications.
Response-to-repeatability of quantitative imaging features for longitudinal response assessment (2018)

Quantitative imaging biomarkers (QIBs) are often selected and ranked based on their repeatability performance. In the context of treatment response assessment, however, one must also consider how sensitive a QIB is to measuring changes in the tumour. This work introduces response-to-repeatability ratio (R/R), which weighs the ability of a QIB to detect significant changes with respect to its measurement repeatability and applies it to the case of PET texture features. R/R is evaluated as the proportion of measurable changes from baseline to follow-up for each candidate QIB. We analyse 47 texture features extracted from lesions in bone-metastatic prostate cancer patients who received double baseline and/or baseline to treatment follow-up <sup>18</sup>F-NaF PET/CT scans. R/R evaluates the proportion of follow-up changes outside of the 95% limits of agreement (LOA) defined by test-retest values. Intraclass correlation coefficient (ICC) and coefficient of variation (CV) are calculated for each feature. Relationship between ICC and R/R are evaluated with the Spearman's correlation coefficient. R/R varied significantly across texture features: 41/47 (87%) features demonstrated R/R > 5%; 21/47 (45%) features demonstrated R/R > 10%, and 11/47 (23%) features demonstrated R/R > 20%. LOA of features ranged from [0.998, 1.001] to [0.22, 4.86]. Repeatability alone did not qualify a feature for its efficacy at detecting measurable change at follow-up, as shown by weak correlations between R/R and both CV and ICC (ρ = 0.23 and ρ = 0.40, respectively). Three features demonstrated excellent ICC (ICC > 0.75) and R/R greater than that of SUV<sub>max</sub> (R/R = 41.8%): skewness (ICC = 0.92, R/R = 75.4%), kurtosis (ICC = 0.88, R/R = 47.0%) and diagonal moment (ICC = 0.88, R/R = 45.5%). R/R characterizes the sensitivity of candidate QIBs to detect measurable changes at follow-up. R/R supplements existing precision performance metrics (e.g. CV, ICC, and LOA) as an index to assess the utility of QIBs for response assessment.
Growth and structural characterization of epitaxial (La1−xLux)2O3 layers grown on Si(111) (2010)

The authors study the growth and structure of epitaxial (La1−xLux)2O3 alloy layers on Si(111) in either homogeneous or digital alloy form. Layer-by-layer growth is achieved by thermal evaporation from La and Lu oxides at a substrate temperature of 700 °C. The grown structures have an abrupt Si/oxide interface as observed by grazing incidence x-ray diffraction and transmission electron microscopy. The in-plane lattice parameter of the (La1−xLux)2O3 reaches values within 0.2% of Si. In-plane lattice constants determined by density functional theory are only slightly off Vegard’s law whereas larger deviations are found for the out-of-plane direction. This may explain the different in-plane lattice constants they measure for digitally or randomly grown (La1−xLux)2O3.
Address extraction: a graph matching and ontology-based approach to conceptual information retrieval (2005)

Address and related location-awareness information can be retrieved and extracted from the Web using content-based IR technologies. Much recent research on content-based information retrieval focuses on conceptual analysis of unstructured texts on the Web. This paper illustrates an address extraction application to achieve an ontology-based conceptual IR system with graph matching. Our key idea is that a document can be represented as a sub-graph of a predefined ontology graph. An approximate graph matching approach is used for content (address) extraction. This work is part of an ongoing project to develop an intelligent search agent to support driving-related information extraction from the Web.
Zusammenfassung (1973)

Die eingesetzte spitzenlose Kurzhubhonmaschine wurde zunächst statisch und dynamisch untersucht, um Schwachstellen zu bestimmen und Möglichkeiten zu deren Beseitigung aufzuzeigen.
Sll0528, a Site-2-Protease, Is Critically Involved in Cold, Salt and Hyperosmotic Stress Acclimation of Cyanobacterium Synechocystis sp. PCC 6803 (2014)

Site-2-proteases (S2Ps) mediated proteolysis of transmembrane transcriptional regulators is a conserved mechanism to regulate transmembrane signaling. The universal presence of S2P homologs in different cyanobacterial genomes suggest conserved and fundamental functions, though limited data has been available. Here we provide the first evidence that Sll0528, a site-2-protease in Synechocystis sp. PCC 6803 is crucial for salt, cold and hyperosmotic stress acclimation. Remarkable induction of sll0528 gene expression was observed under salt, cold and hyperosmotic stress, much higher than induction of the other three S2Ps. Knock-out of sll0528 gene in wild type Synechocystis sp. PCC 6803 increased their sensitivity to salt, cold and hyperosmotic stress, as revealed by retarded growth, reduced pigments and disrupted photosystems. The sll0528 gene was induced to a much smaller extent by high light and mixotrophic growth with glucose. Similar growth responses of the sll0528 knockout mutant and wild type under high light and mixotrophic growth indicated that sll0528 was dispensable for these conditions. Recombinant Sll0528 protein could cleave beta-casein into smaller fragments. These results together suggest that the Sll0528 metalloprotease plays a role in the stress response and lays the foundation for further investigation of its mechanism, as well as providing hints for the functional analysis of other S2Ps in cyanobacteria.
Design of human granzyme B variants resistant to serpin B9 (2012)

Human granzyme B (hGB) is a serine protease involved in immune-mediated apoptosis. Its cytotoxicity makes it potentially applicable in cancer therapy. However, the effectiveness of hGB can be hampered by the cytosolic expression of a natural protein inhibitor, human Serpin B9 (hSB9). Here, we used computational approaches to identify hGB mutations that can affect its binding to hSB9 without significantly decreasing its catalytic efficiency. Alanine-scanning calculations allowed us to identify residues of hGB important for the interaction with hSB9. Some variants were selected, and molecular dynamic simulations on the mutated hGB in complex with hSB9 in aqueous solution were carried out to investigate the effect of these variants on the stability of the complex. The R28K, R201A, and R201K mutants significantly destabilized the interaction of the protein with hSB9. Consistently, all of these variants also retained their activity in the presence of the Serpin B9 inhibitor in subsequent in vitro assays of wild-type and mutated hGB. In particular, the activity of R201K hGB with and without Serpin B9 is very similar to that of the wild-type protein. Hence, R201K hGB emerges as a promising species for antitumoral therapy applications.
Transition to miscibility in a binary Bose–Einstein condensate induced by linear coupling (2005)

A one-dimensional mean-field model of a two-component condensate in the parabolic trap is considered, with the components corresponding to different spin states of the same atom. We demonstrate that the linear coupling (interconversion) between them, induced by a resonant electromagnetic wave, can drive the immiscible binary condensate into a miscible state. This transition is predicted in an analytical form by means of a variational approximation (for an infinitely long system), and is confirmed by direct numerical solutions of the symmetric and asymmetric models (the asymmetry accounts for a possible difference in the chemical potential between the components). We define an order parameter of the system as an off-centre shift of the centre of mass of each component. A numerically found dependence of the order parameter on the linear-coupling strength reveals a second-kind phase transition (in an effectively finite system). The phase transition looks very similar in two different regimes, namely, with a fixed number of atoms, or a fixed chemical potential. An additional transition is possible between double- and single-humped density distributions in the weak component of a strongly asymmetric system. We also briefly consider dynamical states, with the two components oscillating relative to each other. In this case, the components periodically separate even if they should be mixed in the static configuration.
Minimizing area and maximizing porosity for cell layouts using innovative routing strategies (2002)

This paper presents an enhanced maze routing algorithm to get a dense yet porous cell layout, which is electromigration and latch-up safe, for 'tall cell' (high performance) architectures. By placing ports at the most optimal location, discouraging routing between two ports and preventing vertical routes from blocking ports at the edge of the cell we ensure that the layout has minimum area and maximum routability. By encouraging power routing in diffusion and restricting use of metal near the power bus, we provide free tracks for through the cell routing by chip level router. By placing bulk contacts between shared diffusions and choosing proper well/substrate contacts, we prevent any latch-up problems. We also ensure that the nets carrying high drive currents are EM safe by routing them with wider (non-default) wires. These automation strategies enabled us to achieve production quality layout for around 80% of core cells of a high performance ASIC library. The result was minimization of layout generation time (as no manual intervention was necessary) leading to a faster ASIC library development cycle.
High Levels of Antibody to Panton‐Valentine Leukocidin Are Not Associated with Resistance toStaphylococcus aureus–Associated Skin and Soft‐Tissue Infection (2010)

Neutralizing antibody to PVL does not protect children against primary or recurrent CA-MRSA-associated SSTI.
Clinical advances in gene therapy updates on clinical trials of gene therapy in haemophilia (2019)

Gene therapy is rapidly becoming a new therapeutic strategy for haemophilia A and B treatment. In the 1990s, studies in animal models showed that adeno-associated vectors (AAV) exhibited an efficient expression of factor IX (FIX). In the first clinical trial in patients with haemophilia B, therapeutic levels of FIX were documented but the expression remained only for few weeks. Subsequently, improvements in vector design, such as the use of different AAV serotypes, the development of the self-complementary vector, the engineering of the transgene with codon optimization and liver-specific expression cassette resulted in circulating FIX level between 2% and 5% for long-lasting period. Recently, a natural gain of function FIX variant (Padua) inserted in the F9 cDNA improved the expression of FIX achieving a level of more than 30% resulting in cessation of infusions and in a greatly reduction of bleeding events. Encouraging clinical progresses have been also obtained from trials of gene therapy for haemophilia A. Transgene expression persisted for three years with circulating FVIII activity levels of 52.3% in patients treated with AAV vector containing a codon-optimized F8 cDNA. A complication, reported in both clinical trials for haemophilia A and B, was the elevation of liver enzymes, which resolved with steroid treatment in a large group of patients. However, to date, the pathophysiological mechanism for the liver toxicity remains still unclear. Clinical trials with adeno-associated vectors have documented a significant success for haemophilia gene therapy demonstrating potential to transform haemophilia treatment offering hope for a long-term expression.
Parameters for accurate genome alignment (2010)

These results enable more accurate genome alignment, with reliability measures for local alignments and for individual aligned bases. This study was made possible by our new software, LAST, which can align vertebrate genomes in a few hours http://last.cbrc.jp/.
Self-supervised Data Bootstrapping for Deep Optical Character\n Recognition of Identity Documents (2019)

The essential task of verifying person identities at airports and national\nborders is very time consuming. To accelerate it, optical character recognition\nfor identity documents (IDs) using dictionaries is not appropriate due to high\nvariability of the text content in IDs, e.g., individual street names or\nsurnames. Additionally, no properties of the used fonts in IDs are known.\nTherefore, we propose an iterative self-supervised bootstrapping approach using\na smart strategy to mine real character data from IDs. In combination with\nsynthetically generated character data, the real data is used to train\nefficient convolutional neural networks for character classification serving a\npractical runtime as well as a high accuracy. On a dataset with 74 character\nclasses, we achieve an average class-wise accuracy of 99.4 %. In contrast, if\nwe would apply a classifier trained only using synthetic data, the accuracy is\nreduced to 58.1 %. Finally, we show that our whole proposed pipeline\noutperforms an established open-source framework\n
Nitecapone: a nitric oxide radical scavenger. (1994)

Nitecapone [3-(3,4-dihydroxy-5-nitrobenzylidene)-2,4-pentanedione], is a scavenger of nitric oxide produced in vitro. It reduced the rate of methemoglobin formation from oxyhemoglobin exposed to nitric oxide generated from the reaction of hydroxylamine with Complex I of catalase and it decreased the amount of nitrite formed in the reaction of oxygen with nitric oxide generated from sodium nitroprusside. Nitecapone also affected the L-arginine dependent accumulation of nitrite in a suspension of peritoneal rat neutrophils. The related compounds entacapone [2-cyano-N, N-diethyl-3-(3,4 dihydroxy-5-nitrobenzyl)-propenamide] and OR 1246 [3-(3,4-dihydroxy-5-nitrobenzyl)-2,4-pentanedione] were also able to scavenge nitric oxide. The action of nitecapone on nitric oxide expands the role of nitecapone as a scavenger of reactive oxygen species, and suggests nitecapone, entacapone and OR 1246 as potential therapeutic agents for the treatment of diseases connected with increased production of nitric oxide.
Mesangial cell-derived interleukin-10 modulates mesangial cell response to lipopolysaccharide. (1995)

Interleukin (IL)-10 is a novel cytokine produced by a variety of cells, including monocytes/macrophages, upon exposure to lipopolysaccharide (LPS). Recent observations indicate that, in turn, IL-10 exerts suppressive effects on macrophage response to LPS. Because mesangial cells are also a target for LPS, we have examined the potential role of IL-10 in the regulation of mesangial cell response to LPS. To this aim, we have studied the synthesis and the autocrine/paracrine function of IL-10 in cultured mouse mesangial cells. IL-10 mRNA expression and IL-10 protein secretion were determined by a reverse transcription polymerase chain reaction technique and a specific enzyme-linked immunosorbent assay, respectively. No IL-10 mRNA expression was detectable in unactivated cells. LPS induced IL-10 mRNA expression in a dose-dependent fashion (1 to 100 micrograms/ml). In addition, LPS induced IL-10 protein release that was both dose dependent (1 to 100 micrograms/ml) and time dependent (24 to 72 hours). We have also studied the effect of IL-10 on the production of inflammatory mediators by LPS-activated mouse mesangial cells. Whereas recombinant IL-10 inhibited the generation of tumor necrosis factor-alpha (TNF-alpha) and IL-1 beta by 90 and 60%, respectively, it did not affect the formation of nitric oxide-derived nitrite (NO2-) and nitrate (NO3-). As shown by the use of anti-IL-10 monoclonal antibody, endogenously produced IL-10 affected the generation of TNF-alpha but neither that of IL-1 beta nor that of NO2- and NO3-. Finally, we have examined whether conditions known to also reduce the generation of TNF-alpha modified the expression of IL-10. Of all the conditions tested, only the addition of desferrioxamine and transforming growth factor-beta were found to increase IL-10 release. Together, these data demonstrate that mesangial cell-derived IL-10 has important regulatory effects on the inflammatory response of these cells to LPS because of its capacity to blunt TNF-alpha generation.
Multidrug and Toxic Compound Extrusion-Type Transporters Implicated in Vacuolar Sequestration of Nicotine in Tobacco Roots (2008)

Nicotine is a major alkaloid accumulating in the vacuole of tobacco (Nicotiana tabacum), but the transporters involved in the vacuolar sequestration are not known. We here report that tobacco genes (NtMATE1 and NtMATE2) encoding transporters of the multidrug and toxic compound extrusion (MATE) family are coordinately regulated with structural genes for nicotine biosynthesis in the root, with respect to spatial expression patterns, regulation by NIC regulatory loci, and induction by methyl jasmonate. Subcellular fractionation, immunogold electron microscopy, and expression of a green fluorescent protein fusion protein all suggested that these transporters are localized to the vacuolar membrane. Reduced expression of the transporters rendered tobacco plants more sensitive to the application of nicotine. In contrast, overexpression of NtMATE1 in cultured tobacco cells induced strong acidification of the cytoplasm after jasmonate elicitation or after the addition of nicotine under nonelicited conditions. Expression of NtMATE1 in yeast (Saccharomyces cerevisiae) cells compromised the accumulation of exogenously supplied nicotine into the yeast cells. The results imply that these MATE-type proteins transport tobacco alkaloids from the cytosol into the vacuole in exchange for protons in alkaloid-synthesizing root cells.