gebhart/patrepeval huggingface dataset:
Liquid structure of the choline chloride-urea deep eutectic solvent (reline) from neutron diffraction and atomistic modelling (2016)

The structure of 1 : 2 choline chloride : urea (reline) deep eutectic solvent has been determined, showing extensive hydrogen bonding between all species.
The Effects of Phosphorylation on the Structure and Function of Proteins (1993)

Many bacterial clustered regularly interspaced short palindromic repeats (CRISPR)–CRISPR-associated (Cas) systems employ the dual RNA–guided DNA endonuclease Cas9 to defend against invading phages and conjugative plasmids by introducing site-specific ...Read More
Synthesis and Photovoltaic Application of Copper(I) Sulfide Nanocrystals (2008)

We present the rational synthesis of colloidal copper(I) sulfide nanocrystals and demonstrate their application as an active light absorbing component in combination with CdS nanorods to make a solution-processed solar cell with 1.6% power conversion efficiency on both conventional glass substrates and flexible plastic substrates with stability over a 4 month testing period.
Impact of Bt Cottons Expressing One or Two Insecticidal Proteins of <I>Bacillus thuringiensis</I> Berliner on Growth and Survival of Noctuid (Lepidoptera) Larvae (2001)

A series of laboratory assays were performed to compare the relative impact of commercial and experimental cultivars of cotton, Gossypium hirsutum (L.), expressing zero, one, or two insecticidal proteins of Bacillus thuringiensis Berliner, on several lepidopteran pests. Assays in which larvae were fed fresh plant tissue indicated that dual-toxin B. thuringiensis (Bt) cultivars, expressing both Cry1Ac and Cry2Ab endotoxins of B. thuringiensis, were more toxic to bollworms, Helicoverpa zea (Boddie), fall armyworms, Spodoptera frugiperda (J. E. Smith), and beet armyworms, Spodoptera exigua (Hubner), than single-toxin cultivars expressing Cry1Ac. Assays in which lyophilized plant tissue was incorporated into artificial diet also indicated improved activity of the dual-toxin Bt cultivar compared with single-toxin plants. Both bollworm and tobacco budworm, Heliothis virescens (F.), growth was reduced by Bt cotton, particularly the dual-toxin cultivar. Although assays with lyophilized tissues were done using largely sublethal doses, bollworm survival was reduced by the dual-toxin cultivar. It appears that this newly developed Bt cotton expressing two toxins will be more effective and have a wider range of activity on these lepidopteran pests.
Co‐localization of endomorphin‐2 and substance P in primary afferent nociceptors and effects of injury: a light and electron microscopic study in the rat (2004)

Endomorphin-2 (EM2) is a tetrapeptide with remarkable affinity and selectivity for the mu-opioid receptor. In the present study, we used double-fluorescence and electron microscopic immunocytochemistry to identify subsets of EM2-expressing neurons in dorsal root ganglia and spinal cord dorsal horn of adult rats. Within the lumbar dorsal root ganglia, we found EM2 immunoreactivity mainly in small-to-medium size neurons, most of which co-expressed the neuropeptide substance P (SP). In adult rat L4 dorsal root ganglia, 23.9% of neuronal profiles contained EM2 immunoreactivity and ranged in size from 15 to 36 microM in diameter (mean 24.3 +/- 4.3 microM). Double-labelling experiments with cytochemical markers of dorsal root ganglia neurons showed that approximately 95% of EM2-immunoreactive cell bodies also label with SP antisera, 83% co-express vanilloid receptor subtype 1/capsaicin receptor, and 17% label with isolectin B4, a marker of non-peptide nociceptors. Importantly, EM2 immunostaining persisted in mice with a deletion of the preprotachykinin-A gene that encodes SP. In the lumbar spinal cord dorsal horn, EM2 expression was concentrated in presumptive primary afferent terminals in laminae I and outer II. At the ultrastructural level, electron microscopic double-labelling showed co-localization of EM2 and SP in dense core vesicles of lumbar superficial dorsal horn synaptic terminals. Finally, 2 weeks after sciatic nerve axotomy we observed a greater than 50% reduction in EM2 immunoreactivity in the superficial dorsal horn. We suggest that the very strong anatomical relationship between primary afferent nociceptors that express SP and EM2 underlies an EM2 regulation of SP release via mu-opioid autoreceptors.
GPR119, a novel G protein‐coupled receptor target for the treatment of type 2 diabetes and obesity (2007)

GPR119 is a G protein-coupled receptor expressed predominantly in the pancreas (beta-cells) and gastrointestinal tract (enteroendocrine cells) in humans. De-orphanization of GPR119 has revealed two classes of possible endogenous ligands, viz., phospholipids and fatty acid amides. Of these, oleoylethanolamide (OEA) is one of the most active ligands tested so far. This fatty acid ethanolamide is of particular interest because of its known effects of reducing food intake and body weight gain when administered to rodents. Agonists at the GPR119 receptor cause an increase in intracellular cAMP levels via G(alphas) coupling to adenylate cyclase. In vitro studies have indicated a role for GPR119 in the modulation of insulin release by pancreatic beta-cells and of GLP-1 secretion by gut enteroendocrine cells. The effects of GPR119 agonists in animal models of diabetes and obesity are reviewed, and the potential value of such compounds in future therapies for these conditions is discussed.
Highly degenerate, inosine-containing primers specifically amplify rare cDNA using the polymerase chain reaction (1988)

Journal Article Highly degenerate, inosine-containing primers specifically amplify rare cDNA using the polymerase chain reaction Get access Karen Knoth, Karen Knoth 2Department of Pharmacology, Vanderbilt Medical SchoolNashville, TN, 37232, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Steven Roberds, Steven Roberds 2Department of Pharmacology, Vanderbilt Medical SchoolNashville, TN, 37232, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Celeste Poteet, Celeste Poteet 1Department of Molecular Physiology and Biophysics, Vanderbilt Medical SchoolNashville, TN, 37232, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Michael Tamkun Michael Tamkun 1Department of Molecular Physiology and Biophysics, Vanderbilt Medical SchoolNashville, TN, 37232, USA2Department of Pharmacology, Vanderbilt Medical SchoolNashville, TN, 37232, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 16, Issue 22, 25 November 1988, Page 10932, https://doi.org/10.1093/nar/16.22.10932 Published: 25 November 1988 Article history Received: 11 October 1988 Published: 25 November 1988
Expression of the FMS/KIT-like gene FLT3 in human acute leukemias of the myeloid and lymphoid lineages (1992)

FLT3, a receptor belonging to the FMS/KIT family and localized to 13q12, could play a role in the biology of early hematopoietic progenitor cells. Because FMS and KIT are expressed in both normal progenitors and myeloid leukemias, we looked for FLT3 expression in fresh human leukemic cells using Northern blot analysis. High levels of FLT3 expression were detected in 92% of the cases of acute myeloid leukemia (AML) tested, ranging from the M1 to the M5 stages of differentiation assessed in the French-American-British classification. Immature (MO) AML cells, biphenotypic leukemias, and AML with megakaryocytic differentiation (M7 subtype) also expressed the FLT3 transcript. FLT3 was also expressed at high levels in acute lymphoid leukemias of T and B origins. Finally, it was not expressed in chronic myeloid leukemias in chronic phase, whereas it was expressed in most blast crisis samples. This pattern of expression of FLT3 contrasts with the expression of FMS and KIT restricted to myeloid leukemias, and suggests that the FLT3 product could play a role in the expansion of the leukemic blasts of both the myeloid and lymphoid lineages.
Control of autoantibody affinity by selection against amino acid replacements in the complementarity-determining regions. (1994)

Rheumatoid factor (RF) autoantibodies can be produced in healthy individuals after infections or immunizations and thus escape normal tolerization mechanisms. It has not been clear whether such autoantibodies can undergo somatic hypermutation and affinity maturation similar to antibodies to exogenous antigens. We have investigated how these autoantibodies are regulated in normal individuals by analyzing the sequences of monoclonal IgM RFs obtained as hybridomas from donors after immunization. The variable regions undergo extensive hypermutation, but in contrast to antibodies against exogenous antigens, there is a strong selection against mutations that result in replacement of amino acids in the hypervariable, or complementarity-determining, regions. Furthermore, we found no increase in affinity of these RFs with the accumulation of mutations. This suggests that high-affinity variants are tolerized during the hypermutation process and there is a peripheral mechanism operating on certain autoreactive B cells that, while not deleting or anergizing all autoreactive cells, prevents the generation of high-affinity autoantibodies. Comparison of RFs by using the VH1 DP-10 heavy chain variable region segment from both normal individuals and rheumatoid arthritis (RA) patients suggests that RF from RA patients may not be subject to such a controlling mechanism.
Effect of active immunization against oestradiol in developing ram lambs on plasma gonadotrophin and testosterone concentrations, time of onset of puberty and testicular blood flow (1995)

Merino ram lambs were actively immunized against oestradiol-6 (o-carboxy methyl) oxime-BSA conjugate at 14 weeks of age and received a booster injection 4 weeks later. This treatment led to an increase in plasma concentrations of gonadotrophin and tended to enhance the increase in testicular volume until 26 weeks of age; however, testis size and mass at time of castration (30 weeks of age) were similar to values in BSA-immunized lambs. Detrimental effects were observed in some oestradiol-immunized ram lambs, for example a steep decline in testicular volume towards the end of the experiment, the presence of large vacuoles within the seminiferous epithelium and, in one lamb, few germ cell at 30 weeks of age. Testicular blood plasma flow was significantly reduced in oestradiol-immunized lambs (P < 0.01). The steroidogenic function of the testis was markedly enhanced in oestradiol-immunized lambs as reflected by high plasma concentrations of testosterone measured at 22, 26 and 30 weeks of age and by high testosterone production calculated from blood flow and venous-arterial differences at 30 weeks of age. Nevertheless, total live mass gain over the 16 week study was not increased in oestradiol-immunized lambs. Testicular biopsies were taken at 22 and 26 weeks of age in half of the lambs in each treatment group. Testicular volume measured at castration was decreased in control lambs in which biopsies were taken (P < 0.05), and plasma concentrations of testosterone measured at 30 weeks of age were significantly lower in oestradiol-immunized lambs in which biopsies were taken (P < 0.02) compared with lambs in which no biopsy had been taken. It is concluded that active immunization against oestradiol in ram lambs does not advance the time of onset of puberty and does not confer any reproductive or maturational advantages.
Studies on nucleosides and nucleotides. LXXXVII. Purine cyclonucleosides. XLII. Synthesis of 2'-deoxy-2'-fluoroguanosine. (1981)

2'-Deoxy-2'-fluoroguanosine (VII) was synthesized starting from 8, 2'-anhydro-8-oxy-9-β-D-arabinofuranosylguanine (8, 2'-O-cycloguanosine) (I). Compound I was protected at 2-NH2 with an isobutyryl group and at 3'- and 5'-OH with tetrahydrofuranyl groups. The protected compound III was derivatized to the arabino nucleoside V and thence converted to VII by treatment with trifluoromethanesulfonyl chloride and tetra-n-butylammonium fluoride. The resulting 2'-deoxy-2'-fluoroguanosine showed a 3'-endo favored conformation.
Vpr protein of human immunodeficiency virus type 1 forms cation-selective channels in planar lipid bilayers. (1996)

A small (96-aa) protein, virus protein R (Vpr), of human immunodeficiency virus type 1 contains one hydrophobic segment that could form a membrane-spanning helix. Recombinant Vpr, expressed in Escherichia coli and purified by affinity chromatography, formed ion channels in planar lipid bilayers when it was added to the cis chamber and when the trans chamber was held at a negative potential. The channels were more permeable to Na+ than to Cl- ions and were inhibited when the trans potential was made positive. Similar channel activity was caused by Vpr that had a truncated C terminus, but the potential dependence of channel activity was no longer seen. Antibody raised to a peptide mimicking part of the C terminus of Vpr (AbC) inhibited channel activity when added to the trans chamber but had no effect when added to the cis chamber. Antibody to the N terminus of Vpr (AbN) increased channel activity when added to the cis chamber but had no effect when added to the trans chamber. The effects of potential and antibodies on channel activity are consistent with a model in which the positive C-terminal end of dipolar Vpr is induced to traverse the bilayer membrane when the opposite (trans) side of the membrane is at a negative potential. The C terminus of Vpr would then be available for interaction with AbC in the trans chamber, and the N terminus would be available for interaction with AbN in the cis chamber. The ability of Vpr to form ion channels in vitro suggests that channel formation by Vpr in vivo is possible and may be important in the life cycle of human immunodeficiency virus type 1 and/or may cause changes in cells that contribute to AIDS-related pathologies.
Polyvinylpyrrolidone (PVP) in nanoparticle synthesis (2015)

Colloidal synthesis offers a route to nanoparticles (NPs) with controlled composition and structural features. This Perspective describes the use of polyvinylpyrrolidone (PVP) to obtain such nanostructures. PVP can serve as a surface stabilizer, growth modifier, nanoparticle dispersant, and reducing agent. As shown with examples, its role depends on the synthetic conditions. This dependence arises from the amphiphilic nature of PVP along with the molecular weight of the selected PVP. These characteristics can affect nanoparticle growth and morphology by providing solubility in diverse solvents, selective surface stabilization, and even access to kinetically controlled growth conditions. This Perspective includes discussions of the properties of PVP-capped NPs for surface enhanced Raman spectroscopy (SERS), assembly, catalysis, and more. The contribution of PVP to these properties as well as its removal is considered. Ultimately, the NPs accessed through the use of PVP in colloidal syntheses are opening new applications, and the concluding guidelines provided herein should enable new nanostructures to be accessed facilely.
MicroRNA-21 Regulates Non-Small Cell Lung Cancer Cell Invasion and Chemo-Sensitivity through SMAD7 (2016)

Carboplatin may upregulate SMAD7 through suppression of miR-21 to inhibit TGFβ receptor signaling mediated NSCLC cell invasion.
Application of Paper-Supported Printed Gold Electrodes for Impedimetric Immunosensor Development (2012)

In this article, we report on the formation and mode-of-operation of an affinity biosensor, where alternate layers of biotin/streptavidin/biotinylated-CRP-antigen/anti-CRP antibody are grown on printed gold electrodes on disposable paper-substrates. We have successfully demonstrated and detected the formation of consecutive layers of supra-molecular protein assembly using an electrical (impedimetric) technique. The formation process is also supplemented and verified using conventional surface plasmon resonance (SPR) measurements and surface sensitive characterization techniques, such as X-ray photoelectron spectroscopy (XPS) and atomic force microscopy (AFM). The article provides a possible biosensor development scheme, where-(1) fabrication of paper substrate (2) synthesis of gold nanoparticle inks (3) inkjet printing of gold electrodes on paper (4) formation of the biorecognition layers on the gold electrodes and (5) electrical (impedimetric) analysis of growth-all are coupled together to form a test-structure for a recyclable and inexpensive point-of-care diagnostic platform.
Hybrid approach of video indexing and machine learning for rapid indexing and highly precise object recognition (2002)

Video database and object recognition have been treated as separate problems in the past. Previous retrieval applications achieved rapid indexing and robust retrieval capabilities, but the precision of recognizing objects in video images is lower than object recognition using machine learning. In contrast with video retrieval, machine learning needs vast computational training time in advance and cannot handle similarity easily. To solve this problem, we present an image-based video recognition framework combined with video retrieval and object recognition. To develop an effective combination, we evaluated several retrieval methods and the support vector machine (SVM), which is one of the most popular supervised learning techniques. From experimental results, we found that the combination of extended color-pair retrieval and SVM using color location is the most effective pair for high precision and rapid indexing of a video recognition system.
In Vivo Results of a New Focal Tissue Ablation Technique: Irreversible Electroporation (2006)

This paper reports results of in vivo experiments that confirm the feasibility of a new minimally invasive method for tissue ablation, irreversible electroporation (IRE). Electroporation is the generation of a destabilizing electric potential across biological membranes that causes the formation of nanoscale defects in the lipid bilayer. In IRE, these defects are permanent and lead to cell death. This paper builds on our earlier theoretical work and demonstrates that IRE can become an effective method for nonthermal tissue ablation requiring no drugs. To test the capability of IRE pulses to ablate tissue in a controlled fashion, we subjected the livers of male Sprague-Dawley rats to a single 20-ms-long square pulse of 1000 V/cm, which calculations had predicted would cause nonthermal IRE. Three hours after the pulse, treated areas in perfusion-fixed livers exhibited microvascular occlusion, endothelial cell necrosis, and diapedeses, resulting in ischemic damage to parenchyma and massive pooling of erythrocytes in sinusoids. However, large blood vessel architecture was preserved. Hepatocytes displayed blurred cell borders, pale eosinophilic cytoplasm, variable pyknosis and vacuolar degeneration. Mathematical analysis indicates that this damage was primarily nonthermal in nature and that sharp borders between affected and unaffected regions corresponded to electric fields of 300-500 V/cm.
Biyolojik silah olarak hemorajik fever virusları: Teşhis, tedavi ve kontrol (2005)

Hemorajik Fever Virus (HFV)’lari, zoonotik ozellik tasiyip insanlarda “Viral Hemorajik Fever Sendromu” na neden olurlar. Bu viruslar icinde arenaviruslar, bunyaviruslar, flaviviruslar ve filoviruslar yer almaktadir. HFV’lari, Rusya, Amerika Birlesik Devletleri ve Kuzey Kore tarafindan biyolojik silah olarak kullanilmistir. Bu derlemede, biyolojik silah ajani olarak kullanilan ve biyoterorizme hizmet edebilecek HFV’lari icin cesitli kamu, ozel ve askeri kurum ve kuruluslarca uygulanilan ve yeni gelistirilen teshis, tedavi ve kontrol yontemleri aciklanmistir
Simian immunodeficiency virus as a model of human HIV disease (1999)

Because of strong clinical, pathological, virological and immunological analogies with HIV infection of humans, infection of macaques with SIV provides a valuable model for exploring crucial issues related to both the pathogenesis and prevention of HIV infection. The model has offered a unique setting for the preclinical evaluation of drugs, vaccines and gene-therapies against HIV, and has helped to identify many virus and host determinants of lentiviral disease. For instance, the importance of an intact nef gene for efficient lentivirus replication and disease induction, and the protective ability of live attenuated, nef-deleted viruses have been first demonstrated in macaques using molecular clones of SIV. More recently, the development of chimeric HIV-SIV vectors able to establish infection and induce disease in macaques has provided new opportunities for the evaluation of vaccination strategies based upon HIV antigens. The aim of this review is to describe the natural course of SIV infection in macaques and to outline how this model has contributed to our understanding of the complex interaction between lentiviruses and host immune system.
An Autocompensating Quantum Key Distribution System Using Polarization Splitting of Light (1998)

Quantum cryptographic key distribution (QKD) systems1 transmit cryptographic key data encoded in the quantum states of individual optical photons with security of the data guaranteed by the fundamental quantum properties of light, rather than by computational complexity or barriers to interception. Beamsplitter attacks are avoided by using single photons, while attempts to read and replace the photons with copies are thwarted by randomly switching between two non-orthogonal bases for the photon states. This so-called 4-state protocol1 forces an eavesdropper trying to read-and-replace photons to induce errors at a minimum rate of about 25%, which can be readily detected by the parties exchanging the key data. Several groups have performed QKD experiments that demonstrate its feasibility2.
SU‐E‐T‐130: Are Proton Gantries Needed? An Analysis of 4332 Patient Proton Gantry Treatment Plans From the Past 10 Years (2015)

Purpose: To ascertain the necessity of a proton gantry, as compared to the feasibility of using a horizontal fixed proton beam‐line for treatment with advanced technology. Methods: To calculate the percentage of patients that can be treated with a horizontal fixed beam‐line instead of a gantry, we analyze the distributions of beam orientations of our proton gantry patients treated over the past 10 years. We identify three horizontal fixed beam geometries (FIXED, BEND and MOVE) with the patient in lying and/or sitting positions. The FIXED geometry includes only table/chair rotations and translations. In BEND, the beam can be bent up/down for up to 20 degrees. MOVE allows for patient head/body angle adjustment. Based on the analysis, we select eight patients whose plan involves beams which are still challenging to achieve with a horizontal fixed beam. These beams are removed in the pencil beam scanning (PBS) plan optimized for the fixed beam‐line (PBS‐fix). We generate non‐coplanar PBS‐gantry plans for comparison, and perform a robustness analysis. Results: The percentage of patients with head‐and‐neck/brain tumors that can be treated with horizontal fixed beam is 44% in FIXED, 70% in 20‐degrees BEND, and 100% in 90‐degrees MOVE. For torso regions, 99% of the patients can be treated in 20‐degree BEND. The target coverage is more homogeneous with PBS‐fix plans compared to the clinical scattering treatment plans. The PBS‐fix plans reduce the mean dose to organs‐at‐risk by a factor of 1.1–28.5. PBS‐gantry plans are as good as PBS‐fix plans, sometimes marginally better. Conclusion: The majority of the beam orientations can be realized with a horizontal fixed beam‐line. Challenging non‐coplanar beams can be eliminated with PBS delivery. Clinical implementation of the proposed fixed beam‐line requires use of robotic patient positioning, further developments in immobilization, and image guidance. However, our results suggest that fixed beam‐lines can be as effective as gantries.