gebhart/patrepeval huggingface dataset:
Chemical composition and biological functions of Listeria monocytogenes cell wall preparations (1983)

A crude Listeria cell wall fraction, a purified fraction (PF) with demonstrated biological activity, as well as a third fraction of base-hydrolyzed PF (BHPF) were analyzed for chemical composition and activities not previously described. Listeria cell wall fraction and PF contained significant quantities of lipid, whereas BHPF was lipid depleted. Fatty acid compositions were typical of gram-positive bacteria. PF and BHPF were depleted in protein. Alanine, glutamic acid, diaminopimelic acid, glucosamine, and muramic acid were found in all fractions, in enhanced concentration in PF and BHPF, and with molar ratios typical of bacterial peptidoglycans. Major neutral sugars were rhamnose, ribose, ribitol, and glucose. The concentrations of rhamnose, ribose, and glucose were increased in BHPF. Differences in chemical composition of the fractions reflected differences in their biological activities: Listeria cell wall fraction induced resistance to Listeria infection, whereas PF did not. Mitogenic and adjuvant activities were demonstrated for Listeria cell wall fraction and PF but were lost in BHPF. BHPF retained the ability to induce macrophage-mediated tumoricidal activity and decrease resistance to Listeria infection.
Enduring epigenetic landmarks define the cancer microenvironment (2018)

The growth and progression of solid tumors involves dynamic cross-talk between cancer epithelium and the surrounding microenvironment. To date, molecular profiling has largely been restricted to the epithelial component of tumors; therefore, features underpinning the persistent protumorigenic phenotype of the tumor microenvironment are unknown. Using whole-genome bisulfite sequencing, we show for the first time that cancer-associated fibroblasts (CAFs) from localized prostate cancer display remarkably distinct and enduring genome-wide changes in DNA methylation, significantly at enhancers and promoters, compared to nonmalignant prostate fibroblasts (NPFs). Differentially methylated regions associated with changes in gene expression have cancer-related functions and accurately distinguish CAFs from NPFs. Remarkably, a subset of changes is shared with prostate cancer epithelial cells, revealing the new concept of tumor-specific epigenome modifications in the tumor and its microenvironment. The distinct methylome of CAFs provides a novel epigenetic hallmark of the cancer microenvironment and promises new biomarkers to improve interpretation of diagnostic samples.
Dual Character of Arduengo Carbene–Radical Adducts: Addition versus Coordination Product (2007)

Zwei Grundtypen von Radikaladdukten wurden bei der Addition von Radikalen an ein stabiles N-heterocyclisches Carben erhalten. (iPrO)2(O)P. und [(CO)5Re.] lieferten die Additionsprodukte, bei [(CO)5Mn.] und [(CO)3CpMo.] (Cp=η5-Cyclopentadienyl) dagegen wurde ein Carbonylligand ersetzt, und durch Koordination an das Metallzentrum entstanden neuartige metallzentrierte Radikale (siehe Schema).
Monitoring bridge scour using fiber optic sensors. (2015)

The scouring process excavates and carries away materials from the bed and banks of streams, and from around the piers and abutments of bridges. Scour undermines bridges and may cause bridge failures due to structural instability. In the last 30 years, more than 1,000 bridges collapsed in the U.S. and about 60% of the failures are related to the scour of bridge foundations. Due to the difficulty in inspecting bridge scour, scour-induced failures tend to occur suddenly without prior warning or signs of distress to the structures. Owing to the threat of hurricane-induced flooding and the fact that there are a significant number of coastal and river/bayou bridges in Louisiana, a more reliable inspection and monitoring procedure for bridge scour is needed. This proposed study is to develop bridge scour monitoring techniques using fiber optic sensors. Based on theoretical and numerical studies, a few mechanisms were proposed for foundation scour monitoring and verified in laboratory tests. In order to apply those mechanisms to field bridges, three instrumentations were designed and tested, and one design was selected for field applications. According to the selected design, two 18-ft long piles with Fiber Bragg Grating (FBG) sensors were then fabricated, transported, and installed beside the foundation of the field bridge. Finally, the long-term monitoring was conducted to evaluate the foundation scour condition.
SIMPLE mutation in demyelinating neuropathy and distribution in sciatic nerve (2004)

Charcot-Marie-Tooth neuropathy type 1C (CMT1C) is an autosomal dominant demyelinating peripheral neuropathy caused by missense mutations in the small integral membrane protein of lysosome/late endosome (SIMPLE) gene. To investigate the prevalence of SIMPLE mutations, we screened a cohort of 152 probands with various types of demyelinating or axonal and pure motor or sensory inherited neuropathies. SIMPLE mutations were found only in CMT1 patients, including one G112S and one W116G missense mutations. A novel I74I polymorphism was identified, yet no splicing defect of SIMPLE is likely. Haplotype analysis of STR markers and intragenic SNPs linked to the gene demonstrated that families with the same mutation are unlikely to be related. The clustering of the G112S, T115N, and W116G mutations within five amino acids suggests this domain may be critical to peripheral nerve myelination. Electrophysiological studies showed that CMT1C patients from six pedigrees (n = 38) had reduced nerve conduction velocities ranging from 7.5 to 27.0m/sec (peroneal). Two patients had temporal dispersion of nerve conduction and irregularity of conduction slowing, which is unusual for CMT1 patients. We report the expression of SIMPLE in various cell types of the sciatic nerve, including Schwann cells, the affected cell type in CMT1C.
Small Incision Lenticule Extraction (SMILE) versus Femtosecond Laser-Assisted In Situ Keratomileusis (FS-LASIK) for Myopia: A Systematic Review and Meta-Analysis (2016)

In conclusion, both FS-LASIK and SMILE are safe, effective and predictable surgical options for treating myopia. However, dry eye symptoms and loss of corneal sensitivity may occur less frequently after SMILE than after FS-LASIK.
ZnGeP2 Parametric Amplifier (1995)

Both pumped induced loss and parametric amplification have been observed in ZnGeP2. A single pass, small signal gain of 10 has been observed with a 2.064 μm pump beam. A significant pump induced loss has been observed and characterized at the signal wavelength.
Efficacy of Simultaneous Intradermal Vaccination of Swine against Porcine Circovirus 2, Porcine Reproductive and Respiratory Syndrome Virus, Mycoplasma hyopneumoniae and Lawsonia intracellularis (2021)

The combined application of vaccines in swine offers many benefits, including reduced time and labour costs, and improved animal welfare, due to fewer injections and manipulations. This study investigated if simultaneous intradermal vaccinations against porcine circovirus 2, porcine reproductive and respiratory syndrome virus, <i>Mycoplasma hyopneumoniae</i>, and <i>Lawsonia intracellularis</i>, using a specialised needle-free applicator would confer comparable protection against experimental infection compared to the single vaccines. In all cases, the administration of the vaccines together was as efficacious as the administration of the vaccines alone, significantly reducing clinical signs associated with each of the four pathogens.
Characterization and chromosome location of the gene GSTZ1 encoding the human Zeta class glutathione transferase and maleylacetoacetate isomerase (1998)

The Zeta class of cytosolic glutathione-S-transferases (GSTs) has recently been identified and spans a range of species from plants to humans. The cDNA and protein of a human member of this class have been previously characterised in our laboratory. This cDNA has also been described as maleylacetoacetate isomerase (MAAI), an enzyme of the phenylalanine catabolism pathway (Fernandez-Canon and Penalva, 1998). The present study has determined the structure and chromosome location of the gene encoding human GSTZ1/MAAI. The gene spans approximately 10.9 kb and is composed of 9 exons. Three intron positions of GSTZ1 were precisely conserved compared to the carnation and Caenorhabditis elegans Zeta GST genes. Fluorescent in situ hybridization mapped the gene to a single locus on chromosome 14q24.3, which is in agreement with an independent localization between the Genethon markers D14S263 and D14S67. The coding region of the gene differed from the GSTZ1 cDNA at two nucleotide positions in exon 3, resulting in Lys-32-->Glu and Arg-42--> Gly substitutions. This gene structure information will allow analysis of the polymorphism in genomic DNA samples, and enables further investigations into genetic defects in this step of the phenylalanine catabolism pathway.
Effect of Carbon Content on Deep Drawability of Rimmed Steel Sheet (1970)

T he deep drawability (R.-value) was studied in rimmed steel sheets melted in air. The variables examined were the carbon content, the cold rolling reduction (50 to 90% ), and the annealing conditions (700 0 and 800 0 e X 5 hr in non-decarburizing atmosphere or 750 0 e X 10 hr in decarburizing atmosphere).
Faculty Opinions recommendation of Time of Disease-Modifying Antirheumatic Drug Start in Juvenile Idiopathic Arthritis and the Likelihood of a Drug-Free Remission in Young Adulthood. (2021)

Read the full review for this Faculty Opinions recommended article: Time of Disease-Modifying Antirheumatic Drug Start in Juvenile Idiopathic Arthritis and the Likelihood of a Drug-Free Remission in Young Adulthood.
Lightweight lexical source model extraction (1996)

Software engineers maintaining an existing software system often depend on the mechanized extraction of information from system artifacts. Some useful kinds of information—source models—are well known: call graphs, file dependences, etc. Predicting every kind of source model that a software engineer may need is impossible. We have developed a lightweight approach for generating flexible and tolerant source model extractors from lexical specifications. The approach is lightweight in that the specifications are relatively small and easy to write. It is flexible in that there are few constraints on the kinds of artifacts from which source models are extracted (e.g., we can extract from source code, structured data files, documentation, etc.). It is tolerant in that there are few constraints on the condition of the artifacts. For example, we can extract from source that cannot necessarily be compiled. Our approach extended the kinds of source models that can be easily produced from lexical information while avoiding the constraints and brittleness of most parser-based approaches. We have developed tools to support this approach and applied the tools to the extraction of a number of different source models (file dependences, event interactions, call graphs) from a variety of system artifacts (C, C++, CLOS, Eiffel. TCL, structured data). We discuss our approach and describe its application to extract source models not available using existing systems; for example, we compute the implicitly-invokes relation over Field tools. We compare and contrast our approach to the conventional lexical and syntactic approaches of generating source models.
Heparan sulfate proteoglycans (HSPGs) and chondroitin sulfate proteoglycans (CSPGs) function as endocytic receptors for an internalizing anti-nucleic acid antibody (2017)

A subset of monoclonal anti-DNA autoantibodies enters a variety of living cells. Here, we aimed to identify the endocytic receptors recognized by an internalizing anti-nucleic acid autoantibody, the 3D8 single-chain variable fragment (scFv). We found that cell surface binding and internalization of 3D8 scFv were inhibited markedly in soluble heparan sulfate (HS)/chondroitin sulfate (CS)-deficient or -removed cells and in the presence of soluble HS and CS. 3D8 scFv colocalized intracellularly with either HS proteoglycans (HSPGs) or CSPGs in HeLa cells. 3D8 scFv was co-endocytosed and co-precipitated with representative individual HSPG and CSPG molecules: syndecan-2 (a transmembrane HSPG), glypican-3 (a glycosylphosphatidylinositol (GPI)-anchored HSPG); CD44 (a transmembrane CSPG); and brevican (a GPI-anchored CSPG). Collected data indicate that 3D8 scFv binds to the negatively charged sugar chains of both HSPGs and CSPGs and is then internalized along with these molecules, irrespective of how these proteoglycans are associated with the cell membrane. This is the first study to show that anti-DNA antibodies enter cells via both HSPGs and CSPGs simultaneously. The data may aid understanding of endocytic receptors that bind anti-DNA autoantibodies. The study also provides insight into potential cell membrane targets for macromolecular delivery.
Cardiomyocyte Regeneration (2017)

Author(s): Eschenhagen, Thomas; Bolli, Roberto; Braun, Thomas; Field, Loren J; Fleischmann, Bernd K; Frisén, Jonas; Giacca, Mauro; Hare, Joshua M; Houser, Steven; Lee, Richard T; Marbán, Eduardo; Martin, James F; Molkentin, Jeffery D; Murry, Charles E; Riley, Paul R; Ruiz-Lozano, Pilar; Sadek, Hesham A; Sussman, Mark A; Hill, Joseph A
A novel photoacoustic nanoprobe of ICG@PEG-Ag2S for atherosclerosis targeting and imaging in vivo (2016)

Atherosclerosis is a major cause of cardiovascular and cerebrovascular diseases that have high mortality and disability rates. Because of its unclear pathogenic mechanism and heterogeneous distribution feature, it is still a big challenge to achieve precise diagnosis and therapy of atherosclerosis at its early stage in vivo. Herein, we fabricated a new ICG@PEG-Ag2S nanoprobe by a simple self-assembly of DT-Ag2S QDs, amphipathic C18/PEG polymer molecules and ICG. The ICG@PEG-Ag2S nanoprobe showed relatively long blood retention and was selectively accumulated in the region of atherosclerotic plaque due to the lipophilicity of the C18 chain to the atherosclerosis microenvironment, and thus the atherosclerosis was real-time monitored by high contrast-enhanced photoacoustic (PA) imaging of ICG. Combining the high signal-to-noise ratio (SNR) and high spatial resolution fluorescence imaging of Ag2S QDs in the second near-infrared window (NIR-II) and related histological assessment in vitro, the feasibility of this new nanoprobe for atherosclerosis targeting in an Apoe(-/-) mouse model was verified. Additionally, hemolysis and coagulation assays of the ICG@PEG-Ag2S revealed its decent hemocompatibility and no histological changes were observed in the main organs of the mouse. Such a simple, multifunctional nanoprobe for targeting and PA imaging of atherosclerosis will have a great potential for future clinical applications.
Cellular chromophores and signaling in low level light therapy (2007)

The use of low levels of visible or near infrared light (LLLT) for reducing pain, inflammation and edema, promoting healing of wounds, deeper tissues and nerves, and preventing tissue damage by reducing cellular apoptosis has been known for almost forty years since the invention of lasers. Originally thought to be a peculiar property of laser light (soft or cold lasers), the subject has now broadened to include photobiomodulation and photobiostimulation using non-coherent light. Despite many reports of positive findings from experiments conducted in vitro, in animal models and in randomized controlled clinical trials, LLLT remains controversial. This likely is due to two main reasons; firstly the biochemical mechanisms underlying the positive effects are incompletely understood, and secondly the complexity of rationally choosing amongst a large number of illumination parameters such as wavelength, fluence, power density, pulse structure and treatment timing has led to the publication of a number of negative studies as well as many positive ones. In recent years major advances have been made in understanding the mechanisms that operate at the cellular and tissue levels during LLLT. Mitochondria are thought to be the main site for the initial effects of light and specifically cytochrome c oxidase that has absorption peaks in the red and near infrared regions of the electromagnetic spectrum matches the action spectra of LLLT effects. The discovery that cells employ nitric oxide (NO) synthesized in the mitochondria by neuronal nitric oxide synthase, to regulate respiration by competitive binding to the oxygen binding of cytochrome c oxidase, now suggests how LLLT can affect cell metabolism. If LLLT photodissociates inhibitory NO from cytochrome c oxidase, this would explain increased ATP production, modulation of reactive oxygen species, reduction and prevention of apoptosis, stimulation of angiogenesis, increase of blood flow and induction of transcription factors. In particular, signaling cascades are initiated via cyclic adenosine monophosphate (cAMP) and nuclear factor kappa B (NF-&kgr;B). These signal transduction pathways in turn lead to increased cell proliferation and migration (particularly by fibroblasts), modulation in levels of cytokines, growth factors and inflammatory mediators, and increases in anti-apoptotic proteins. The results of these biochemical and cellular changes in animals and patients include such benefits as increased healing in chronic wounds, improvements in sports injuries and carpal tunnel syndrome, pain reduction in arthritis and neuropathies, and amelioration of damage after heart attacks, stroke, nerve injury and retinal toxicity.
Development of a Human Breast-Cancer Derived Cell Line Stably Expressing a Bioluminescence Resonance Energy Transfer (BRET)-Based Phosphatidyl Inositol-3 Phosphate (PIP3) Biosensor (2014)

Stimulation of tyrosine kinase receptors initiates a signaling cascade that activates PI3K. Activated PI3K uses PIP2 to generate PIP3, which recruit Akt to the plasma membrane through its pleckstrin homology (PH) domain, permitting its activation by PDKs. Activated Akt controls important biological functions, including cell metabolism, proliferation and survival. The PI3K pathway is therefore an attractive target for drug discovery. However, current assays for measurement of PIP3 production are technically demanding and not amenable to high-throughput screening. We have established a MCF-7-derived breast cancer cell line, that stably co-expresses the PH domain of Akt fused to Renilla luciferase and YFP fused to a membrane localization signal. This BRET biosensor pair permits to monitor, in real time, in living cells, PIP3 production at the plasma membrane upon stimulation by different ligands, including insulin, the insulin analogue glargine, IGF1, IGF2 and EGF. Moreover, several known inhibitors that target different steps of the PI3K/Akt pathway caused inhibition of ligand-induced BRET. Cetuximab, a humanized anti-EGF receptor monoclonal antibody used for the treatment of cancer, completely inhibited EGF-induced BRET, and the tyrosine kinase inhibitor tyrphostine AG1024 inhibited insulin effect on PIP3 production. Moreover, the effects of insulin and IGF1 were inhibited by molecules that inhibit PI3K catalytic activity or the interaction between PIP3 and the PH domain of Akt. Finally, we showed that human serum induced a dose-dependent increase in BRET signal, suggesting that this stable clone may be used as a prognostic tool to evaluate the PI3K stimulatory activity present in serum of human patients. We have thus established a cell line, suitable for the screening and/or the study of molecules with stimulatory or inhibitory activities on the PI3K/Akt pathway that will constitute a new tool for translational research in diabetes and cancer.
Coherent Singlet-Triplet Oscillations in a Silicon-based Double Quantum Dot (2012)

Exploiting the weak interactions between electron spins and nuclear spins in silicon-based quantum dots leads to a dephasing time two orders of magnitude greater than in analogous gallium-arsenide-based devices, demonstrating the potential of silicon as a host material for quantum information processing.
Characteristics of a High Solar Conversion Efficiency Gallium Arsenide p-n Junction (1960)

The characteristics of high-efficiency gallium arsenide solar cells are reported. Their open-circuit voltage is commonly greater than 0.8 v and the short-circuit current density collected is about one-half that calculated on the basis of absorbed photons. The temperature coefficient for maximum power operation is −0.0036/°C. Both spectral emissivity and spectral response are reported.
Supplementary Table 1 from Chemoprevention of Esophageal Cancer with Black Raspberries, Their Component Anthocyanins, and a Major Anthocyanin Metabolite, Protocatechuic Acid (2023)

&lt;p&gt;PDF file - 52KB, This table includes the primer sequences used for the qPCR analysis done in this study.&lt;/p&gt;
Direct Palladium-Catalyzed Ortho-Arylation of Benzylamines (2006)

[Structure: see text] Unsubstituted benzylamines and N-methylbenzylamine can be ortho-arylated under palladium catalysis at 130 degrees C. The reactions require the presence of trifluoroacetic acid and silver acetate.
Correlation Between Degradation of Bacteriophage T2 Deoxyribonucleic Acid and the Resistance of Escherichia coli to Infection (1969)

The ability of certain strains of Escherichia coli to degrade T2 deoxyribonucleic acid to acid-soluble fragments is correlated with their high capacity to survive T2 infection.
Effect of seed-borne Mycosphaerella pinodes and seed treatments on emergence, foot rot severity, and yield of field pea (2000)

Seed-borne Mycosphaerella pinocles in field pea, its transmission to seedlings, and control by seed treatments were studied under growth room and field conditions. Seeds harvested from naturally infected plants were separated into visibly poor (VP) seeds with lesions, and healthy looking (HL) seeds without lesions. In a controlled environment seed-to-seedling transmission was 67-70% for the HL seeds and 94-100% for the VP seeds. Under field conditions, the percentage of seeds infected by M. pinocles was negatively correlated with seedling emergence (r = -0.939 in 1996. P < 0.01, and r = -0.944 in 1997, P < 0.01) and yield (r = -0.929 in 1996, P < 0.01, and r = -0.757 in 1997, P < 0.05), but there was no relationship with the frequency of foot rot symptoms. When seeds were treated with thiram fungicide or ACM94I bioagent (Glioclaclium roseum), both VP and HL seeds showed increased emergence compared with nontreated controls. Thiram was more effective than ACM941 in improving the emergence, however, neither treatment reduced foot rot severity or increased yield significantly in the two years of field tests
Glyphosate degradation byAgrobacterium radiobacter isolated from activated sludge (1990)

Glidobactins A, B and C are lipopeptide antitumor antibiotics produced by the gliding bacteriumPolyangium brachysporum sp. nov. No. K481-B101. The production of glidobactin A was examined in shake flasks and laboratory fermentors. Medium screening and optimization led to approximately five fold increases in glidobactin A titers in shake flasks and a ten fold increase in titers in 40-1 batch fermentations. Utilization of a stepped glucose feeding protocol resulted in glidobactin A titers of 1860 μg/ml after 144 h of fermentation.
Ruthenium-catalyzed methoxycarbonylation of styrene (2022)

Methoxycarbonylation of styrene in the presence of homogeneous Ru catalysts is reported for the first time. Available Ru3(CO)12 together with halide source such as [bmim]Br, NaBr or LiCl represents active and easy to handle methoxycarbonylation catalyst. The key advantage of the new catalytic systems over traditional Pd catalysts is their high activity at CO pressure as low as 5 bar.