gebhart/patrepeval huggingface dataset:
Design and Synthesis of Motilin Antagonists Derived from the [1−4] Fragment of Porcine Motilin (2002)

A series of cyclic peptides having the general structure H-Phe-c[-N(epsilon)-Lys-X-NH-(CH(2))(n)-CO-] were designed on the basis of structure-activity relationship studies of motilin. All were motilin antagonists. The cyclic peptides, in which X is a 3-tert-butyl-substituted tyrosine residue (H-Phe-c[-N(epsilon)-Lys-Tyr(3-tBu)-beta Ala-] (3), H-Phe-c[-N(epsilon)-Lys-Tyr(3-tBu)-Gly-] (6), H-Phe-c[-N(epsilon)-Lys-Tyr(3-tBu)-Abu-] (7), and H-Phe-c[-N(epsilon)-Lys-Tyr(3-tBu)-Ahx-] (8)) showed potent motilin receptor antagonistic activity in the rabbit smooth muscle (pA(2) > 7). The 3-tert-butyl Tyr was found to be the moiety responsible for enhanced binding to the motilin receptor, while the size of the ring had little importance.
Autoimmune syndrome after induction of neonatal tolerance to alloantigens: analysis of the role of donor T cells in the induction of autoimmunity (1990)

The injection of (C57BL/6 x BALB/c) F1 spleen cells into BALB/c newborn mice leads to activation of persisting F1 donor B cells and development of a lupus-like syndrome in tolerized BALB/c mice. This syndrome is characterized by hypergammaglobulinaemia, high levels of anti-DNA and anti-Sm antibodies, circulating immune complexes and deposits of immunoglobulin in renal glomeruli. The role of donor T cells in this model was investigated by injecting the newborn mice with F1 cells depleted in different T cell subsets by using specific monoclonal antibodies (MoAbs). Tolerance, as shown by an absence of H-2b-specific CTL alloreactivity and persistence of immunoglobulin bearing the donor allotype were observed in mice injected with F1 cells previously depleted in the CD4+ and/or CD8+ T cell subsets as well as in those which received Thy-1+-depleted F1 spleen cells. In these mice, a typical autoimmune syndrome was found, including splenomegaly and lymphadenopathy, anti-ssDNA and anti-aortic myosin IgG antibodies and renal deposition of immunoglobulin. However, some quantitative changes were seen: the levels of anti-aortic myosin antibodies were lower in mice tolerized with CD4+-depleted F1 cells than in those receiving untreated F1 cells. Conversely, higher levels of these autoantibodies were observed in mice tolerized with CD8+-depleted F1 cells. These results suggest that mature donor T cells are not necessary neither for the establishment of neonatal tolerance to alloantigens nor for the activation of F1 donor B cells in the production of the autoimmune syndrome in tolerant mice, but they may contribute in the regulation of the expression of autoreactive B cell clones.
Effects of green manure use on sweet corn root length density under reduced tillage conditions (2006)

A green manure (GM) is a crop grown primarily as a nutrient source and soil amendment for subsequent crops. In environments such as Florida, combined use of GM and reduced tillage may improve soil water and nutrient retention and reduce potential groundwater pollution. In the first 3 years of a long-term experiment, use of GM in a reduced-tillage system on a sandy Florida soil benefited the season-long growth of sweet corn ( Zea mays L. var. Rugosa) much more than final ear yields. To help understand these patterns, we evaluated response of sweet corn roots when in rotation with GM of sunn hemp ( Crotalaria juncea L.; summer) and cahaba white vetch ( Vicia sativa L.; winter 2002–2003) and a multi-species mixture of hairy vetch ( V. villosa Roth.) and cereal rye ( Secale cereale L.; winter 2003–2004). Treatments included sweet corn with combinations of 0 or 133 kg chemical N ha −1 (as NH 4 NO 3 ) and with or without GM. A highly fertilized treatment (267 kg chemical N ha −1 ) without GM was also included. Soil cores were sampled from three depths (0–15, 15–30 and 30–60 cm) both between and within corn rows. Data from two experiments showed that use of GM increased sampled corn root length density (RLD) by 44–54%, although only within the upper 15 cm of soil in one of the two experiments. Corn following GM plus 133 kg chemical N ha −1 produced up to 44% greater RLD than corn with 267 kg chemical N ha −1 . Sampled RLD decreased with distance away from corn plants (from in-row to between-row positions, and from shallow to deeper depth), with roughly 85–95% of sampled RLD existing in the top 30 cm of soil across all treatments. During the 2004 experiment, we found that broadcast, as opposed to banded (placed along corn row only), chemical N application resulted in more even distribution of corn RLD between in-row and between-row positions during late-season without regard to GM crop. Although GM permitted optimal sweet corn growth with a 50% reduction in chemical N application, ear fill during the final 1–2 weeks before harvest may have been reduced in GM treatments. GM effects on the amount and spatial distribution of sweet corn RLD may help explain these trends. Provision of greater N from GM residues and/or altered distribution of supplementary chemical N and irrigation may be required to achieve greater ear yield benefit from GM.
The Landfall and Inland Penetration of a Flood-Producing Atmospheric River in Arizona. Part I: Observed Synoptic-Scale, Orographic, and Hydrometeorological Characteristics (2012)

Abstract Atmospheric rivers (ARs) are a dominant mechanism for generating intense wintertime precipitation along the U.S. West Coast. While studies over the past 10 years have explored the impact of ARs in, and west of, California’s Sierra Nevada and the Pacific Northwest’s Cascade Mountains, their influence on the weather across the intermountain west remains an open question. This study utilizes gridded atmospheric datasets, satellite imagery, rawinsonde soundings, a 449-MHz wind profiler and global positioning system (GPS) receiver, and operational hydrometeorological observing networks to explore the dynamics and inland impacts of a landfalling, flood-producing AR across Arizona in January 2010. Plan-view, cross-section, and back-trajectory analyses quantify the synoptic and mesoscale forcing that led to widespread precipitation across the state. The analyses show that a strong AR formed in the lower midlatitudes over the northeastern Pacific Ocean via frontogenetic processes and sea surface latent-heat fluxes but without tapping into the adjacent tropical water vapor reservoir to the south. The wind profiler, GPS, and rawinsonde observations document strong orographic forcing in a moist neutral environment within the AR that led to extreme, orographically enhanced precipitation. The AR was oriented nearly orthogonal to the Mogollon Rim, a major escarpment crossing much of central Arizona, and was positioned between the high mountain ranges of northern Mexico. High melting levels during the heaviest precipitation contributed to region-wide flooding, while the high-altitude snowpack increased substantially. The characteristics of the AR that impacted Arizona in January 2010, and the resulting heavy orographic precipitation, are comparable to those of landfalling ARs and their impacts along the west coasts of midlatitude continents.
Ferromagnetic resonance and ac conductivity of a polymer composite of Fe3O4 and Fe3C nanoparticles dispersed in a graphite matrix (2004)

Ferromagnetic resonance (FMR) and ac conductivity have been applied to study a polymer composite containing as filler a binary mixture of magnetite (Fe3O4) and cementite (Fe3C) nanoparticles (30–50nm) dispersed in a diamagnetic carbon matrix, which was synthesized by the carburization of nanocrystalline iron. Ac conductivity measurements showed thermally activated behavior involving a range of activation energies and power law frequency dependence at high frequencies similar to conducting polymer composites randomly filled with metal particles. Ferromagnetic resonance measurements revealed a relatively narrow FMR line at high temperatures indicating the presence of ferromagnetic nanoparticles, where thermal fluctuations and interparticle interactions determine the FMR temperature variation. An abrupt change of the FMR spectra was observed at T&amp;lt;81K (ΔT⩽1K) coinciding with a sharp anomaly resolved in the temperature derivative of the ac conductivity. This behavior is attributed to the Verwey transition of Fe3O4 nanoparticles, where the concurrent skin depth variation unveils the FMR of large magnetite conglomerates and thus allows discriminating their contribution from relatively isolated nanoparticles.
Large-Scale Laser Fabrication of Antifouling Silicon-Surface Nanosheet Arrays via Nanoplasmonic Ablative Self-Organization in Liquid CS2 Tracked by a Sulfur Dopant (2018)

Large-scale surface nanopatterning of a commercial silicon (Si) wafer in the form of regular 1D arrays of high-aspect-ratio vertical nanosheets (NSs) for antifouling and other potential promising optoelectronic, nanophotonic, and sensing applications was performed via multishot picosecond IR-laser ablation under a 5-mm-thick carbon disulfide liquid layer. Specifically, the nanopatterned surface layer demonstrates the broad ultralow mid-IR transmittance and the high content of sulfur, carbon, and even oxygen in the modified submicron-thick top layer, preventing the appearance of a Staphylococcus aureus bacterial biofilm. High-resolution transmission electron microscopy studies exhibit the anticorrelating inner versus outer surface abundance of donor sulfur versus adverse carbon and oxygen components and the amorphous structure of the sulfur-hyperdoped NSs atop their crystalline basements. These NSs indicate their appearance via the interfacial vapor/plume bubble-mediated codeposition of Si ablation nanoplumes from the regular trenches and sulfur-containing products of carbon disulfide decomposition in the bubble. Numerical modeling indicates the nanoplasmonic origin of the Si NSs, self-limited in both the 100 nm periods and the submicron heights.
Microalga Chlorella sorokiniana: a new sulfoxidation biocatalyst (2006)

Whole cells of the microalga Chlorella sorokiniana were evaluated in the oxidation of prochiral thioethers as regards conversion, enantiomeric excess and enantioselectivity.
Designing Nanoporous Membranes through Templateless Electropolymerization of Thieno[3,4-b]thiophene Derivatives with High Water Content (2019)

In this work, we present the synthesis of original thieno[3,4-<i>b</i>]thiophene monomers with rigid substituents (e.g., perfluorinated chains, and aromatic groups) and demonstrate the ability to prepare nanotubular and nanoporous structures via templateless, surfactant-free electropolymerization in organic solvents (dichloromethane). For the majority of synthesized monomers, including a significant amount of water in the electropolymerization solvent leads to the formation of nanoporous membranes with tunable size and surface hydrophobicity. If water is not included in the electropolymerization solvent, most of the surfaces prepared are relatively smooth. Tests with different water contents show that the formation of nanoporous membranes pass through the formation of vertically aligned nanotubes and that the increase in water content induces an increase in the number of nanotubes while their diameter and height remain unchanged. An increase in surface hydrophobicity is observed with the formation of nanopores up to ≈300 nm in diameter, but as the nanopores further increase in diameter, the surfaces become more hydrophilic with an observed decrease in the water contact angle. These materials and the ease with which they can be fabricated are extremely interesting for applications in separation membranes, opto-electronic devices, as well as for sensors.
Partial characterization of a cell motility factor from human urine. (1985)

Dialyzed, concentrated urine from 21 patients with a history of bladder cancer or a gross bladder tumor was tested for cell motility activity using BALB/c/3T3 cells. Thirteen urine samples from patients with a gross bladder tumor produced a greater increase in cell migration than 8 urine samples from patients with a history of bladder cancer [167% +/- 14 (S.E.), 64% +/- 19, respectively; p less than 0.001]. Protease treatment of urine from a patient with bladder cancer caused a 95% loss of activity, while heating to 100 degrees for 2 min caused an 86% loss of activity. High-performance liquid chromatography of urine from a patient with bladder cancer revealed that the greatest activity was present in fractions with a molecular weight between 18,000 and 30,000. These results suggest that motility-stimulating factor may be a useful marker for detecting carcinoma of the bladder.
Novel 3-((2-chloroquinolin-3-yl)methylene)indolin-2-one derivatives produce anticancer efficacy in ovarian cancer in vitro (2019)

A novel series of 3-((2-chloroquinolin-3-yl)methylene)indolin-2-ones were synthesized, using the 'molecular hybridization approach' and evaluated for anticancer efficacy. Eleven 3-((2-chloroquinolin-3-yl)methylene)indolin-2-ones (<b>LM01</b> to <b>LM11</b>) were synthesized and evaluated for <i>in vitro</i> cytotoxic efficacy in cancer (ovarian, prostate and colon) and two non-cancerous cell lines. Among the 3-((2-chloroquinolin-3-yl)methylene)indolin-2-one derivatives, <b>LM08,</b> with a 6-Cl substitution in the 3-quinolinyl moiety, had selective and potent cytotoxic efficacy in the ovarian cancer cell line A2780. Further mechanistic investigations indicated that <b>LM08</b> significantly inhibited the clonogenic survival of A2780 cancer cells, which was mediated by inducing apoptosis.
Dynamic slicing method for maintenance of large C programs (2003)

Different program slicing methods are used for maintenance, reverse engineering, testing and debugging. Slicing algorithms can be classified as static slicing and dynamic slicing methods. In several applications the computation of dynamic slices is preferable, since it can produce more precise results. In this paper, we introduce a new forward global method for computing backward dynamic slices of C programs. In parallel to the program execution, the algorithm determines the dynamic slices for any program instruction. We also propose a solution for some problems specific to the C language (such as pointers and function calls). The main advantage of our algorithm is that it can be applied to real-size C programs, because its memory requirements are proportional to the number of different memory locations used by the program (which is in most cases far smaller than the size of the execution history which is, in fact, the absolute upper bound of our algorithm).
Distribution of Peach latent mosaic viroid in Commercial Orchards of Peach in the North of Tunisia (2007)

Abstract The presence of Peach latent mosaic viroid (PLMVd) was monitored during 2 years in peach orchards located in the North of Tunisia. PLMVd population was surveyed using a specific RT‐PCR test adapted to crude sap extract. During the first year (2004), 228 samples were randomly selected in 22 peach orchards (eight cultivars) and tested for the presence of PLMVd. Results showed that PLMVd is highly and equally present in four regions of the North of Tunisia. Analyses of some key factors in relation to PLMVd incidence revealed that the tree age did not influence the infection rate. The eight studied cultivars were clustered in three groups according to their PLMVd incidence. Furthermore, the early and season cultivars were statistically more infected than the late cultivars. Prospections in May and October 2005 were performed in four selected orchards. Each two orchards contained Early May Crest (early cultivar) and Carnival (late cultivar) cultivars, respectively. The difference in PLMVd incidence observed in 2004 was confirmed. Furthermore, no correlation between the tree physiological state and the viroid detection was observed. Further investigations on the origin of the differences in PLMVd incidence between Early May Crest and Carnival cultivars would be of interest.
Automatic detection of invasive ductal carcinoma in whole slide images with convolutional neural networks (2014)

This paper presents a deep learning approach for automatic detection and visual analysis of invasive ductal carcinoma (IDC) tissue regions in whole slide images (WSI) of breast cancer (BCa). Deep learning approaches are learn-from-data methods involving computational modeling of the learning process. This approach is similar to how human brain works using different interpretation levels or layers of most representative and useful features resulting into a hierarchical learned representation. These methods have been shown to outpace traditional approaches of most challenging problems in several areas such as speech recognition and object detection. Invasive breast cancer detection is a time consuming and challenging task primarily because it involves a pathologist scanning large swathes of benign regions to ultimately identify the areas of malignancy. Precise delineation of IDC in WSI is crucial to the subsequent estimation of grading tumor aggressiveness and predicting patient outcome. DL approaches are particularly adept at handling these types of problems, especially if a large number of samples are available for training, which would also ensure the generalizability of the learned features and classifier. The DL framework in this paper extends a number of convolutional neural networks (CNN) for visual semantic analysis of tumor regions for diagnosis support. The CNN is trained over a large amount of image patches (tissue regions) from WSI to learn a hierarchical part-based representation. The method was evaluated over a WSI dataset from 162 patients diagnosed with IDC. 113 slides were selected for training and 49 slides were held out for independent testing. Ground truth for quantitative evaluation was provided via expert delineation of the region of cancer by an expert pathologist on the digitized slides. The experimental evaluation was designed to measure classifier accuracy in detecting IDC tissue regions in WSI. Our method yielded the best quantitative results for automatic detection of IDC regions in WSI in terms of F-measure and balanced accuracy (71.80%, 84.23%), in comparison with an approach using handcrafted image features (color, texture and edges, nuclear textural and architecture), and a machine learning classifier for invasive tumor classification using a Random Forest. The best performing handcrafted features were fuzzy color histogram (67.53%, 78.74%) and RGB histogram (66.64%, 77.24%). Our results also suggest that at least some of the tissue classification mistakes (false positives and false negatives) were less due to any fundamental problems associated with the approach, than the inherent limitations in obtaining a very highly granular annotation of the diseased area of interest by an expert pathologist.
High-Throughput NMR-Based Screening with Competition Binding Experiments (2002)

The Achilles heel of ligand-based NMR screening methods is their failure to detect high-affinity ligands and molecules that bind covalently to the receptor. We have developed a novel approach for performing high-throughput screening with NMR spectroscopy that overcomes this limitation. The method also permits detection of potential high-affinity molecules that are only marginally soluble, thus significantly enlarging the diversity of compounds amenable to NMR screening. The techniques developed utilize transverse and/or selective longitudinal relaxation parameters in combination with competition binding experiments. Mathematical expressions are derived for proper setup of the NMR experiments and for extracting an approximate value of the binding constant for the identified ligand from a single-point measurement. With this approach it is possible to screen thousands of compounds in a short period of time against protein or DNA and RNA fragments. The methodology can also be applied for screening plant and fungi extracts.
Convenient Synthesis of 2‐Benzazepines via Radical Cyclization. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Tunable narrow band THz wave generation from laser induced gas plasma (2010)

Tunable narrowband THz waveforms were generated from laser induced gas plasma using shaped optical pulses. Square wave phase patterns were fed to a spatial light modulator. The frequency and amplitude of the square wave phase were used as parameters to tailor the terahertz waveforms. The dependence of THz waveforms on these parameters has been studied in detail. The presence of the ionization thresholds for pulse shaping is also discussed. We have demonstrated the wide and continuous tunability of the central frequency of the narrowband THz waveform from 2.5 to 7.5THz.
Secreted LasA of Pseudomonas aeruginosa is a staphylolytic protease. (1993)

Full expression of the elastolytic phenotype of Pseudomonas aeruginosa depends on LasA, an extracellular protease with restricted specificity whose mode of action on elastin and biological role is not understood. LasA exhibits amino acid sequence homology to some bacteriolytic proteases and shares several physicochemical properties with the staphylolytic protease of P. aeruginosa. This led us to examine whether the two proteases are the same. Production of LasA and staphylolytic protease by prototrophic and lasA mutant strains of P. aeruginosa was investigated. The two prototrophic strains examined, PAO1 and FRD2, exhibited extracellular staphylolytic activity and secreted LasA. LasA mutants, PAO-E64 lasA1 (Ts), FRD2128 delta lasA, and FRD244 lasA::mTn10, did not exhibit staphylolytic activity. A low level of the LasA protein was detected in the culture filtrate of the temperature-sensitive lasA mutant PAO-E64, but none was detectable in those of the deletion and insertion mutants, FRD2128, and FRD244, respectively. The staphylolytic protease was purified from the culture filtrate of P. aeruginosa strain FRD2 by DEAE-cellulose chromatography. The purified enzyme hydrolyzed pentaglycine into the respective di- and tripeptides and reacted specifically with antibodies against a synthetic peptide identical in sequence to positions 77-98 in LasA. The amino-terminal sequence of the first 15 amino acid residues of the staphylolytic protease was found to be identical with that of the secreted LasA. These results clearly indicate that LasA is a staphylolytic protease. In addition to lysing staphylococci, it may enhance elastolysis by cleaving Gly-Gly bonds, which are abundant in elastin.
Detection of Curvilinear Structures Using the Euclidean Distance Transform. (1998)

In this paper, we present a new method for detecting curvilinear structures in a gray-scale image. The concept of skeleton extraction is introduced to detect more general structures such as tapering structures. A skeleton is extracted from the Euclidean distance map that is constructed based on the edge map of an input image. Then, skeletal points are classified into three types (RIDGE, RAVINE and STAIR), and connected points belonging to the same type are grouped to form a skeletal segment. Our detector satisfies many of desirable properties required of a curvilinear structure detector, and moreover it overcomes some limitations of conventional approaches. 1
Statistical mechanics of matrix models (2004)

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The Role of Endoscopic Retrograde Cholangiopancreatography in the Diagnosis of Biliary Atresia: 14 Years' Experience (2017)

ERCP is safe and accurate in the hands of experts in diagnosing BA if the cause of cholestasis is unclear. While evaluating the role of ERCP for diagnosing this disease, we found that the secondary parameters GGT > 250 U/L, bilirubin > 7.3 mg/dL (125 μmol/L), and the absence of bile traces are risk factors.