gebhart/patrepeval huggingface dataset:
Synthesis and localization of C-type natriuretic peptide in mammalian kidney (1994)

We have previously demonstrated the synthesis of atrial natriuretic factor (ANF) in the distal cortical nephron of the rat kidney. We now report the synthesis of C-type natriuretic peptide (CNP) in the rat, mouse, and human nephron. CNP mRNA was initially detected in the rat and mouse kidney, as well as in three transformed cell lines isolated from the proximal and distal nephron, using reverse transcription-polymerase chain reaction (RT-PCR). Confirmation of the kidney PCR product was performed by nucleotide sequence analysis and Southern hybridization. Northern hybridization of rat brain CNP cDNA to human kidney polyadenylated RNA detected a 1.4-kb gene transcript. Rat nephron segments were microdissected and subjected to RT-PCR to localize CNP mRNA. CNP mRNA was detected in the proximal convoluted tubule, cortical collecting duct, medullary thick limbs, and inner medullary collecting ducts. CNP, as detected by immunohistochemistry, was found to colocalize with CNP mRNA.
Gene Therapy of Cancer with Interleukin-12 (2003)

IL-12 has demonstrated remarkable antitumor activity when used directly as a recombinant protein or when different viral or non-viral vectors transfer its genes. At enhancing tumor immunity, IL-12 acts as a bridge between innate and adaptive immune responses due to its ability to induce proliferation and activation of NK, NKT, and T cells. In addition, IL-12 inhibits tumor angiogenesis mainly through IFN gamma-dependent production of the chemokine IP10. As a result, IL-12 can eliminate several types of tumors developed in rodents. Pre-clinical experience forecasted a quick and successful clinical translation, but the encouraging results observed in animals were not reproduced in patients. Moreover, unacceptable toxicity resulting from IFN gamma overproduction was observed in 2 renal carcinoma patients included in a phase II clinical trial that consisted in systemic administration of rIL-12. As a consequence, development of IL-12 as an antitumor agent was temporarily halted while the high expectations raised among clinicians faded away. Gene transfer methods are designed to confine IL-12 production in the tumor environment preventing systemic toxicity. Tumor cells, dendritic cells, or autologous fibroblasts have been transfected with recombinant adenoviruses or retroviruses to secrete IL-12 locally, showing good efficacy and safety profiles. IL-12 combination with other immunotherapy approaches synergizes to achieve even better results. Encouraging pilot clinical results have been recently obtained from the first phase I trial studying adenovirus mediated in vivo gene transfer of IL-12 into lesions of advanced cancer patients. Further improvements will follow from: i) increases in the efficacy of gene transduction; ii) development of tumor specific promoters; iii) development of regulatable and long-term expression vectors and iv) combination with other immunological and non-immunological anticancer therapies.
Purification of vaccinia virus by zonal centrifugation and analysis of viral protein composition. (1977)

Vaccinia virus propagated in rotated cultures of RK13 cells was purified by sucrose density gradient zonal centrifugation. The purified virus was dissociated with sodium dodecyl sulfate end its protein composition analyzed by polyacrylamide gel electrophoresis. The protein composition of the virion envelope, isolated by the non-ionic detergent Nonidet P-40, was also determined.
Simulations of a Protein Translocation Pore:  SecY (2006)

SecY is the central channel protein of the SecYEbeta translocon, the structure of which has been determined by X-ray diffraction. Extended (15 ns) MD simulations of the isolated SecY protein in a phospholipid bilayer have been performed to explore the relationship between protein flexibility and the mechanisms of channel gating. In particular, principal components analysis of the simulation trajectory has been used to probe the intrinsic flexibility of the isolated SecY protein in the absence of the gamma-subunit (SecE) clamp. Analysis and visualization of the principal eigenvectors support a "plug and clamshell" model of SecY channel gating. The simulation results also indicate that hydrophobic gating at the central pore ring prevents leakage of water and ions through the channel in the absence of a translocating peptide.
Minimal coronary artery damage by myocardial electroporation ablation (2012)

Coronary arteries remain free of clinically relevant damage 3 weeks after epicardial IRE ablation, even amid very large myocardial lesions. This suggests that IRE ablation can be applied safely near or even on coronary arteries. With IRE ablation, arterial blood flow does not appear to affect lesion formation.
Amphetamine-induced psychosis - a separate diagnostic entity or primary psychosis triggered in the vulnerable? (2012)

Use of amphetamine and methamphetamine is widespread in the general population and common among patients with psychiatric disorders. Amphetamines may induce symptoms of psychosis very similar to those of acute schizophrenia spectrum psychosis. This has been an argument for using amphetamine-induced psychosis as a model for primary psychotic disorders. To distinguish the two types of psychosis on the basis of acute symptoms is difficult. However, acute psychosis induced by amphetamines seems to have a faster recovery and appears to resolve more completely compared to schizophrenic psychosis. The increased vulnerability for acute amphetamine induced psychosis seen among those with schizophrenia, schizotypal personality and, to a certain degree other psychiatric disorders, is also shared by non-psychiatric individuals who previously have experienced amphetamine-induced psychosis. Schizophrenia spectrum disorder and amphetamine-induced psychosis are further linked together by the finding of several susceptibility genes common to both conditions. These genes probably lower the threshold for becoming psychotic and increase the risk for a poorer clinical course of the disease.The complex relationship between amphetamine use and psychosis has received much attention but is still not adequately explored. Our paper reviews the literature in this field and proposes a stress-vulnerability model for understanding the relationship between amphetamine use and psychosis.
Regioselective Functionalization. 6.1 Migratory Preferences in Hydroxylamine-O-sulfonic Acid and Schmidt Rearrangements of 7-Substituted Norcamphors (1996)

Hydroxylamine-O-sulfonic acid reacted with syn-7-X- and anti-7-Y-substituted norcamphor derivatives [X = H, OMe, Cl, Br, OTos; Y = H, COOMe, Cl, Br, Tos, COOMe(5-exo-Br)], to give solely bridgehead migrated 2-azalactams, except for minor amounts of methylene migrated 3-azalactams from norcamphor (1) and the syn-7-Br ketone 19. Schmidt reactions of the same ketones provided varying mixtures of methylene and bridgehead migrated lactams, except for norcamphor (1) and anti-7-Br ketone 31, which provided solely 3-azalactams. Significant ratios (>0.4) of bridgehead migration to cleavage products were observed in the Schmidt reactions only with 7-OTos ketones 22 and 24 with exo-5-bromo-anti-7-methoxycarbonyl ketone 37. The Schmidt rearrangements most likely involve iminodiazonium ion intermediates in light of the large amounts of cleavage observed relative to lactam formation and the insensitivity of methylene migration to the substituent size in the reactions of syn-7-substituted norcamphors.
Clonal dominance: cause for a limited and failing immune response to HIV-1 infection and vaccination. (1992)

Oligoclonal and monoclonal antibody populations against different HIV-encoded proteins are common in sera from healthy HIV-1-infected individuals. This is especially important when it includes functional antibody repertoires directed at neutralizing cell free virus or inhibiting cell fusion of virus-infected cells. In the host, during the acute viral syndrome following HIV-1 infection, a rapidly replicating, cell-free and genotypically homogeneous viral population is known to arise from the transmitted viral inoculum. Dominant B and possibly T cell clones responsible for both functional and nonfunctional antibodies appear to arise early in response to this initially homogeneous cell-free viral population heralding seroconversion. During the viremic phase, deposition of cell-free virus as either complement coated or as immune complexes (iccosomes) within the germinal centers results in continued and long-term boosting of primed B cells. This saturation of antigen presenting germinal centers and the presence of limited, immunodominant cross-reactive epitopes on the envelope glycoprotein of the closely-related and immune selected viral quasispecies in the host appear to continue the boosting effect of the primed secondary response. This repertoire freeze appears to be responsible for limiting the recruitment of new uncommitted B cells to other functional epitopes or affinity maturation of B-cell clones to escape variants and the subsequent production and quality of functional antibody against the evolving/selected virus populations. This may include in addition to neutralizing and cell fusion inhibiting antibody, direct complement-fixing and/or NK-directed antibody-dependent cell-mediated antibody as well as various effector, helper, or T cell-mediated activity. In addition to antiviral antibody responses, antibody directed to other invading pathogens or opportunistic organisms may also be clonaly restricted. Antibody facilitating infectivity or blocking effective immunity may also be included in this phenomena and thus be over represented by such a mechanism. AIDS vaccines utilizing the envelope must identify these epitopes to avoid creating clonal dominance and therefore possibly limit the breadth and specificity of a humoral response following infection. Furthermore, immunotherapeutic approaches designed to recruit humoral immune effector function must be able to overcome the dominance of noneffective antibodies and restore a normal polyclonal immune response against HIV. Further research, therefore, into the humoral and cellular dysregulating properties of the HIV-1 envelope is warranted.
Human Gene Encoding the 78,000-Dalton Glucose-Regulated Protein and Its Pseudogene: Structure, Conservation, and Regulation (1988)

The isolation and characterization of a human functional GRP78 gene and a processed pseudogene are described. We present the complete primary structure of the human GRP78 gene, which spans over 5 kb and consists of eight exons. Sequence comparisons reveal that the GRP78 gene shares unusual homology among the human, rat, and hamster in the protein-coding and 3' untranslated regions. In addition, short domains highly conserved with HSP70 isolated from human, Drosophila, Xenopus, yeast, and E. coli DNA are identified within the hydrophobic regions of GRP78. The intronless pseudogene resembles that of a processed gene. It is flanked by a short direct repeat and is embedded within an AT-rich genomic region. The highly active promoter from the functional human GRP78 gene contains a TATA box, five CCAAT sequences, and two potential binding sites for the transcriptional factor Sp1. It consists of a distal domain that enhances basal level expression and a proximal domain essential for responses to calcium ionophore and for a temperature-sensitive mutation which induce the GRP78 gene. Both domains are highly conserved between the rat and the human GRP78 promoters.
4-Acyl Pyrrole Derivatives Yield Novel Vectors for Designing Inhibitors of the Acetyl-Lysine Recognition Site of BRD4(1) (2016)

Several human diseases, including cancer, show altered signaling pathways resulting from changes in the activity levels of epigenetic modulators. In the past few years, small-molecule inhibitors against specific modulators, including the bromodomain and extra-terminal (BET) bromodomain family of acetylation readers, have shown early promise in the treatment of the genetically defined midline carcinoma and hematopoietic malignancies. We have recently developed a novel potent inhibitor of BET proteins, 1 (XD14[ Angew. Chem., Int. Ed. 2013, 52, 14055]), which exerts a strong inhibitory potential on the proliferation of specific leukemia cell lines. In the study presented here, we designed analogues of 1 to study the potential of substitutions on the 4-acyl pyrrole backbone to occupy additional sites within the substrate recognition site of BRD4(1). The compounds were profiled using ITC, DSF, and X-ray crystallography. We could introduce several substitutions that address previously untargeted areas of the substrate recognition site. This work may substantially contribute to the development of therapeutics with increased target specificity against BRD4-related malignancies.
THE VARIABILITY OF FEMORAL ROTATIONAL ALIGNMENT IN TOTAL KNEE ARTHROPLASTY (2005)

Background: Several reference axes are used to establish femoral rotational alignment during total knee arthroplasty, but debate continues with regard to which axis is most accurately and easily identified during surgery. Computer-assisted navigation systems have been developed in an attempt to more accurately and consistently align implants during total knee arthroplasty, but it is unknown if navigation systems can improve the accuracy of femoral rotational alignment as compared with that achieved with more traditional techniques involving mechanical guides. The purposes of the present study were to characterize the variability associated with femoral rotational alignment techniques and to determine whether the use of a computer-assisted surgical navigation system reduced this variability. Methods: Eleven orthopaedic surgeons used five alignment techniques (including one computer-assisted technique and four traditional techniques) to establish femoral rotational alignment axes on ten cadaveric specimens, and the orientation of these axes was recorded with use of a navigation system. These derived axes were compared against a reference transepicondylar axis on each femur that was established after complete dissection of all soft tissues. Results: There was no difference between the mean errors of all five techniques (p > 0.11). Only 17% of the knees were rotated <5° from the reference transepicondylar axis, with alignment errors ranging from 13° of internal rotation to 16° of external rotation. There were significant differences among the surgeons with regard to their ability to accurately establish femoral rotational alignment axes (p < 0.001). Conclusions: All techniques resulted in highly variable rotational alignment, with no technique being superior. This variability was primarily due to the particular surgeon who was performing the alignment procedure. A navigation system that relies on directly digitizing the femoral epicondyles to establish an alignment axis did not provide a more reliable means of establishing femoral rotational alignment than traditional techniques did.
Heterotrimeric G protein signalling in the plant kingdom (2013)

In animals, heterotrimeric G proteins, comprising α-, β-and γ-subunits, perceive extracellular stimuli through cell surface receptors, and transmit signals to ion channels, enzymes and other effector proteins to affect numerous cellular behaviours. In plants, G proteins have structural similarities to the corresponding molecules in animals but transmit signals by atypical mechanisms and effector proteins to control growth, cell proliferation, defence, stomate movements, channel regulation, sugar sensing and some hormonal responses. In this review, we summarize the current knowledge on the molecular regulation of plant G proteins, their effectors and the physiological functions studied mainly in two model organisms: Arabidopsis thaliana and rice (Oryza sativa). We also look at recent progress on structural analyses, systems biology and evolutionary studies.
Somatic Mutations ofEGFRin Colorectal Cancers and Glioblastomas (2004)

To the Editor: Recent reports suggest that mutations in the epidermal growth factor receptor (EGFR) gene predict sensitivity to EGFR kinase inhibitors. In particular, patients with lung cancers containing mutations in the EGFR kinase domain have had responses to gefitinib.1,2 Are similar EGFR mutations present in a significant fraction of other tumor types for which gefitinib might be suitable therapy? To answer this question, we screened DNA from 293 colorectal tumors and 59 glioblastomas for alterations in the EGFR kinase domain (exons 17 to 24). These tumors were chosen for analysis because they have been linked to . . .
Spectroelectrochemical Sensing Based on Multimode Selectivity Simultaneously Achievable in a Single Device. 13. Detection of Aqueous Iron by in Situ Complexation with 2,2‘-Bipyridine (2002)

A spectroelectrochemical sensor with attenuated total reflectance at an indium-doped tin oxide (ITO) optically transparent electrode coated with a thin film of Nafion has been demonstrated for the determination of aqueous iron ion. The novelty of this sensor stems from its ability to take up colorless iron ion (Fe2+) from solution and complex it with an organic ligand, 2,2'-bipyridine (bipy), that has been previously loaded in the optically transparent charge-selective Nafion film coating the electrode. The resulting complex ion, tris(2,2'-bipyridyl)iron(II), Fe(bipy)3(2+), absorbs strongly, making it easily detectable via optical spectroscopy. Fe(bipy)3(2+) loaded into the selective film is oxidized to colorless Fe(bipy)3(3+), which gives rise to an absorbance change for quantifying iron. This paper maps the development of this sensor, from the spectroelectrochemical characterization of the complex ion at an ITO optically transparent electrode to an analysis of the uptake, retention, and optical response of the complex ion in the Nafion film. Finally, an evaluation of the uptake of aqueous Fe2+ by the bipy-loaded Nafion film is reported. These data include preliminary results illustrating the dependence of the sensor response on differing concentrations of Fe2+ in solution.
Expression of functional Bunyamwera virus L protein by recombinant vaccinia viruses (1991)

A cDNA containing the complete coding sequence of the Bunyamwera virus (family Bunyaviridae) L genome segment has been constructed and cloned into two recombinant vaccinia virus expression systems. In the first, the L gene is under control of vaccinia virus P7.5 promoter; in the second, the L gene is under control of the bacteriophage T7 phi 10 promoter, and expression of the L gene requires coinfection with a second recombinant vaccinia virus which synthesizes T7 RNA polymerase. Both systems express a protein which is the same size as the Bunyamwera virus L protein and is recognized by a monospecific L antiserum. The expressed L protein was shown to be functional in synthesizing Bunyamwera virus RNA in a nucleocapsid transfection assay: recombinant vaccinia virus-infected cells were transfected with purified Bunyamwera virus nucleocapsids, and subsequently, total cellular RNA was analyzed by Northern (RNA) blotting. No Bunyamwera virus RNA was detected in control transfections, but in cells which had previously been infected with recombinant vaccinia viruses expressing the L protein, both positive- and negative-sense Bunyamwera virus S segment RNA was detected. The suitability of this system to delineate functional domains within the Bunyamwera virus L protein is discussed.
Off-Resonance Surface-Enhanced Raman Spectroscopy from Gold Nanorod Suspensions as a Function of Aspect Ratio: Not What We Thought (2013)

Design of nanoparticles for surface-enhanced Raman scattering (SERS) within suspensions is more involved than simply maximizing the local field enhancement. The enhancement at the nanoparticle surface and the extinction of both the incident and scattered light during propagation act in concert to determine the observed signal intensity. Here we explore these critical aspects of signal generation and propagation through experiment and theory. We synthesized gold nanorods of six different aspect ratios in order to obtain longitudinal surface plasmon resonances that incrementally spanned 600-800 nm. The Raman reporter molecule methylene blue was trap-coated near the surface of each nanorod sample, generating SERS spectra, which were used to compare Raman signals. The average number of reporter molecules per nanorod was quantified against known standards using electrospray ionization liquid chromatography mass spectrometry. The magnitude of the observed Raman signal is reported for each aspect ratio along with the attenuation due to extinction in suspension. The highest Raman signal was obtained from the nanorod suspension with a plasmon resonance blue-shifted from the laser excitation wavelength. This finding is in contrast to SERS measurements obtained from molecules dried onto the surface of roughened or patterned metal substrates where the maximum observed signal is near or red-shifted from the laser excitation wavelength. We explain these results as a competition between SERS enhancement and extinction, at the excitation and scattered wavelengths, on propagation through the sample.
Is miR-29 an oncogene or tumor suppressor in CLL? (2010)

B-cell chronic lymphocytic leukemia (CLL) is the most common leukemia in the Western world. CLL occurs in two forms, aggressive and indolent. Aggressive CLL is characterized by high ZAP-70 expression and unmutated IgH V(H); indolent CLL shows low ZAP-70 expression and mutated IgH V(H). We recently found that miR-29 is upregulated in indolent human B-CLL, compared to aggressive B-CLL and normal CD19+ B-cells. To determine the role of miR-29 in CLL, we generated transgenic mice overexpressing miR-29 in mouse B-cells. Recently we reported that miR-29 transgenic mice develop indolent CLL phenotype. Interestingly, our previous findings suggest that miR-29 targets expression of TCL1, a critical oncogene in aggressive CLL, indicating that miR-29 might function as a tumor suppressor in CLL. Here we discuss these results and provide additional insights into function of miR-29 in CLL.
Microwave-Assisted Lignin Isolation Using the Enzymatic Mild Acidolysis (EMAL) Protocol (2008)

The use of microwaves is explored in an effort to further improve the recently developed lignin isolation protocol termed EMAL (enzymatic mild acidolysis lignin). Because the presence of the lignin-carbohydrate linkages seems to be rather pronounced within wood, a microwave reactor was used to replace traditional refluxing during the mild acidolysis step. This was done in an attempt to augment the selectivity of this step toward cleaving lignin-carbohydrate bonds as well as reducing the overall intensity of this step toward inducing changes in the lignin structure, thus affording lignin in greater yields and purities. Consequently, in this study the yields, purities, and structures of lignins isolated from spruce (softwood) by the EMAL protocol under various microwave conditions were examined. The variables studied included microwave power, microwave heating time, hydrochloric acid concentration and water content of the reaction medium. Microwave heating afforded EMAL samples of high purity (90%, comparable to the conventional protocol) but in significantly greater gravimetric yields. Quantitative (31)P NMR and SEC data confirmed that the structure of lignin was similar to that obtained by traditional EMALs, with comparable contents of beta-aryl ether bonds, phenolic hydroxyls (condensed and uncondensed), and carboxylic acids.