gebhart/patrepeval huggingface dataset:
Electrotransformation of Clostridium thermocellum (2004)

Electrotransformation of several strains of Clostridium thermocellum was achieved using plasmid pIKm1 with selection based on resistance to erythromycin and lincomycin. A custom-built pulse generator was used to apply a square 10-ms pulse to an electrotransformation cuvette consisting of a modified centrifuge tube. Transformation was verified by recovery of the shuttle plasmid pIKm1 from presumptive transformants of C. thermocellum with subsequent PCR specific to the mls gene on the plasmid, as well as by retransformation of Escherichia coli. Optimization carried out with strain DSM 1313 increased transformation efficiencies from <1 to (2.2 +/- 0.5) x 10(5) transformants per micro g of plasmid DNA. Factors conducive to achieving high transformation efficiencies included optimized periods of incubation both before and after electric pulse application, chilling during cell collection and washing, subculture in the presence of isoniacin prior to electric pulse application, a custom-built cuvette embedded in an ice block during pulse application, use of a high (25-kV/cm) field strength, and induction of the mls gene before plating the cells on selective medium. The protocol and preferred conditions developed for strain DSM 1313 resulted in transformation efficiencies of (5.0 +/- 1.8) x 10(4) transformants per micro g of plasmid DNA for strain ATCC 27405 and approximately 1 x 10(3) transformants per micro g of plasmid DNA for strains DSM 4150 and 7072. Cell viability under optimal conditions was approximately 50% of that of controls not exposed to an electrical pulse. Dam methylation had a beneficial but modest (7-fold for strain ATCC 27405; 40-fold for strain DSM 1313) effect on transformation efficiency. The effect of isoniacin was also strain specific. The results reported here provide for the first time a gene transfer method functional in C. thermocellum that is suitable for molecular manipulations involving either the introduction of genes associated with foreign gene products or knockout of native genes.
Calcitonin/calcitonin gene-related peptide transcription unit: tissue-specific expression involves selective use of alternative polyadenylation sites. (1984)

Different 3' coding exons in the rat calcitonin gene are used to generate distinct mRNAs encoding either the hormone calcitonin in thyroidal C-cells or a new neuropeptide referred to as calcitonin gene-related peptide in neuronal tissue, indicating the RNA processing regulation is one strategy used in tissue-specific regulation of gene expression in the brain. Although the two mRNAs use the same transcriptional initiation site and have identical 5' terminal sequences, their 3' termini are distinct. The polyadenylation sites for calcitonin and calcitonin gene-related peptide mRNAs are located at the end of the exons 4 and 6, respectively. Termination of transcription after the calcitonin exon does not dictate the production of calcitonin mRNA, because transcription proceeds through both calcitonin and calcitonin gene-related peptide exons irrespective of which mRNA is ultimately produced. In isolated nuclei, both polyadenylation sites appear to be utilized; however, the proximal (calcitonin) site is preferentially used in nuclei from tissues producing calcitonin mRNA. These data suggest that the mechanism dictating production of each mRNA involves the selective use of alternative polyadenylation sites.
Intraocular lens calculation adjustment after laser refractive surgery using Scheimpflug imaging (2016)

No author has a financial or proprietary interest in any material or method mentioned.
Cambinol, a Novel Inhibitor of Neutral Sphingomyelinase 2 Shows Neuroprotective Properties (2015)

Ceramide is a bioactive lipid that plays an important role in stress responses leading to apoptosis, cell growth arrest and differentiation. Ceramide production is due in part to sphingomyelin hydrolysis by sphingomyelinases. In brain, neutral sphingomyelinase 2 (nSMase2) is expressed in neurons and increases in its activity and expression have been associated with pro-inflammatory conditions observed in Alzheimer's disease, multiple sclerosis and human immunodeficiency virus (HIV-1) patients. Increased nSMase2 activity translates into higher ceramide levels and neuronal cell death, which can be prevented by chemical or genetic inhibition of nSMase2 activity or expression. However, to date, there are no soluble, specific and potent small molecule inhibitor tool compounds for in vivo studies or as a starting point for medicinal chemistry optimization. Moreover, the majority of the known inhibitors were identified using bacterial, bovine or rat nSMase2. In an attempt to identify new inhibitor scaffolds, two activity assays were optimized as screening platform using the recombinant human enzyme. First, active hits were identified using a fluorescence-based high throughput compatible assay. Then, hits were confirmed using a 14C sphingomyelin-based direct activity assay. Pharmacologically active compounds and approved drugs were screened using this strategy which led to the identification of cambinol as a novel uncompetitive nSMase2 inhibitor (Ki = 7 μM). The inhibitory activity of cambinol for nSMase2 was approximately 10-fold more potent than for its previously known target, silence information regulator 1 and 2 (SIRT1/2). Cambinol decreased tumor necrosis factor-α or interleukin-1 β-induced increases of ceramide and cell death in primary neurons. A preliminary study of cambinol structure and activity allowed the identification of the main structural features required for nSMase2 inhibition. Cambinol and its analogs may be useful as nSMase2 inhibitor tool compounds to prevent ceramide-dependent neurodegeneration.
Biosynthesis of thyrotropin-releasing hormone by a rat medullary thyroid carcinoma cell line. (1988)

Prepro-thyrotropin-releasing hormone (TRH) messenger RNA was detected in the rat medullary thyroid carcinoma cell line CA77. The RNA of 1.6 kilobases comigrated with that found in rat hypothalamus. Using three radioimmunoassays specific for pro-TRH-derived peptides, we demonstrated that CA77 cells synthesize high levels of immunoreactive TRH and all of the other pro-TRH-derived peptides identified in hypothalamic tissue. The relative levels of the pro-TRH-derived peptides also indicate that CA77 cells process the TRH precursor in a manner similar to hypothalamic tissue. CA77 cells provide a promising model system for further studies of prepro-TRH gene regulation and post-translational maturation.
Sex differences in primary Sjögren's syndrome. (1999)

This study indicates that women may have more positive serological findings than men and a higher prevalence of fatigue. No sex differences could be established with other extraglandular manifestations of SS.
mRNA on the Move: The Road to Its Biological Destiny (2013)

Cells have evolved to regulate the asymmetric distribution of specific mRNA targets to institute spatial and temporal control over gene expression. Over the last few decades, evidence has mounted as to the importance of localization elements in the mRNA sequence and their respective RNA-binding proteins. Live imaging methodologies have shown mechanistic details of this phenomenon. In this minireview, we focus on the advanced biochemical and cell imaging techniques used to tweeze out the finer aspects of mechanisms of mRNA movement.
Peptide-based immunotherapeutic approaches to glioma: a review (2007)

Despite advances in surgery, radiation and chemotherapy, the prognosis of patients with malignant glioma is still very poor; therefore, the development of a novel therapeutic modality is essential. There are increasing reports demonstrating that systemic immunotherapy using dendritic cells or a peptide vaccine is capable of inducing an antiglioma response. Peptide-based immunotherapy strategies appear promising as an approach to successfully induce an antitumor immune response and prolong survival in patients with glioma without major side effects. Now, peptide-based immunotherapy could be a new treatment modality for patients with brain tumors.
PEEP—A rapid chemical‐shift imaging method (1989)

Abstract The phase‐encoded echo‐planar (PEEP) technique, a variant of echo‐planar imaging, is used to achieve simultaneous high‐speed spatial and chemical‐shift data acquisition. This technique is the 2DFT equivalent of the projection reconstruction echo‐planar method for chemical‐shift imaging. Examples of images and spectra obtained using the PEEP method are presented. © 1989 Academic Press, Inc.
SIK2 Is Critical in the Regulation of Lipid Homeostasis and Adipogenesis In Vivo (2014)

Cyclic AMP promotes chronic expression of target genes mainly by protein kinase A-dependent activation of CREB transcription factor machineries in the metabolic tissues. Here, we wanted to elaborate whether CREB-regulated transcription factor (CRTC)2 and its negative regulator salt-inducible kinase (SIK)2 are involved in the transcriptional control of the metabolic pathway in adipocytes. SIK2 knockout (SIK2 KO) mice exhibited higher blood glucose levels that were associated with impaired glucose and insulin tolerance. Hypertriglyceridemia was apparent in SIK2 KO mice, mainly due to the increased lipolysis from white adipocytes and the decreased fatty acid uptake in the peripheral tissues. Investigation of white adipocytes revealed the increases in fat cell size and macrophage infiltration, which could be linked to the metabolic anomaly that is associated in these mice. Interestingly, SIK2 KO promoted the enhancement in the CRTC2-CREB transcriptional pathway in white adipocytes. SIK2 KO mice displayed increased expression of activating transcription factor (ATF)3 and subsequent downregulation of GLUT4 expression and reduction in high-molecular weight adiponectin levels in the plasma, leading to the reduced glucose uptake in the muscle and white adipocytes. The effect of SIK2-dependent regulation of adipocyte metabolism was further confirmed by in vitro cell cultures of 3T3 L1 adipocytes and the differentiated preadipocytes from the SIK2 or CRTC2 KO mice. Collectively, these data suggest that SIK2 is critical in regulating whole-body glucose metabolism primarily by controlling the CRTC2-CREB function of the white adipocytes.
Characterization of H2 Binding Sites in Prototypical Metal−Organic Frameworks by Inelastic Neutron Scattering (2005)

The hindered rotor transitions of H(2) adsorbed in the chemically related and prototypical porous metal-organic frameworks IRMOF-1, IRMOF-8, IRMOF-11, and MOF-177 were studied by inelastic neutron scattering to gain information on the specifics of H(2) binding in this class of adsorbents. Remarkably sharp and complex spectra of these materials signify a diversity of well-defined binding sites. Similarities in the spectral features as a function of H(2) loading and correlations with recent crystallographic studies were used to assign transitions ranging in rotational barrier from <0.04 to 0.6 kcal/mol as corresponding to localized adsorption sites on the organic and inorganic components of these frameworks. We find that binding of H(2) at the inorganic cluster sites is affected by the nature of the organic link and is strongest in IRMOF-11 in accord with our adsorption isotherm data. The sites on the organic link have lower binding energies, but a much greater capacity for increases in H(2) loading, which demonstrates their importance for hydrogen uptake by these materials.
Identification of V3 Loop-binding Proteins as Potential Receptors Implicated in the Binding of HIV Particles to CD4+Cells (1998)

The binding of human immunodeficiency virus (HIV) type 1 particles to CD4(+) cells could be blocked either by antibodies against the V3 loop domain of the viral external envelope glycoprotein gp120, or by the V3 loop mimicking pseudopeptide 5[Kpsi(CH2N)PR]-TASP, which forms a stable complex with a cell-surface-expressed 95-kDa protein. Here, by using an affinity matrix containing 5[Kpsi(CH2N)PR]-TASP and cytoplasmic extracts from human CEM cells, we purified three V3 loop-binding proteins of 95, 40, and 30 kDa, which after microsequencing were revealed to be as nucleolin, putative HLA class II-associated protein (PHAP) II, and PHAP I, respectively. The 95-kDa cell-surface protein was also isolated and found to be nucleolin. We show that recombinant preparations of gp120 bind the purified preparations containing the V3 loop-binding proteins with a high affinity, comparable to the binding of gp120 to soluble CD4. Such binding is inhibited either by 5[Kpsi(CH2N)PR]-TASP or antibodies against the V3 loop. Moreover, these purified preparations inhibit HIV entry into CD4(+) cells as efficiently as soluble CD4. Taken together, our results suggest that nucleolin, PHAP II, and PHAP I appear to be functional as potential receptors in the HIV binding process by virtue of their capacity to interact with the V3 loop of gp120.
Thermochromic Block Copolymer Photonic Gel (2008)

ADVERTISEMENT RETURN TO ISSUEPREVCommunication to the...Communication to the EditorNEXTThermochromic Block Copolymer Photonic GelJongseung Yoon†, Wonmok Lee‡, and Edwin L. Thomas*View Author Information Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge Massachusetts 02139* Corresponding author. E-mail: [email protected]†Present address: Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana−Champaign, Urbana, IL 61801.‡Present address: Department of Chemistry, Sejong University, 98 Gunja-dong, Gwangjin-gu, Seoul, Korea 143-747.Cite this: Macromolecules 2008, 41, 13, 4582–4584Publication Date (Web):June 13, 2008Publication History Received28 April 2008Revised30 May 2008Published online13 June 2008Published inissue 1 July 2008https://pubs.acs.org/doi/10.1021/ma8009504https://doi.org/10.1021/ma8009504rapid-communicationACS PublicationsCopyright © 2008 American Chemical SocietyRequest reuse permissionsArticle Views1945Altmetric-Citations61LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Copolymers,Optical properties,Photonics,Solvents,Thickness Get e-Alerts
Azido‐tetrazolo isomerizations of some thiazolopyridines (1977)

Abstract 2‐Azidothiazolo[5,4‐ b ]pyridine and 2‐azidothiazolo[4,5‐ c ]pyridine were synthesized. Azido‐tetrazolo isomerizations of these compounds were investigated and in both cases also the tetrazolo form could be obtained. In solution, equilibria at different temperatures were determined.
Multilayered Cobalt Oxide Platelets for Negative Electrode Material of a Lithium-Ion Battery (2008)

Layer-controllable CoO and platelets were prepared by calcination of hexagonal , which was synthesized via a surfactant-free hydrothermal method. As negative electrode material for lithium-ion batteries, CoO and platelets demonstrated high reversible capacity (more than for CoO and for ) and excellent electrochemical cycling stability. The multilayered CoO platelets showed larger capacity and much better cycling performance than the monolayer CoO platelets and CoO nanoparticles. The effect of dimension and morphology of CoO particles on the electrode behavior was discussed.
Sox6 enhances erythroid differentiation in human erythroid progenitors (2011)

Sox6 belongs to the Sry (sex-determining region Y)-related high-mobility-group-box family of transcription factors, which control cell-fate specification of many cell types. Here, we explored the role of Sox6 in human erythropoiesis by its overexpression both in the erythroleukemic K562 cell line and in primary erythroid cultures from human cord blood CD34+ cells. Sox6 induced significant erythroid differentiation in both models. K562 cells underwent hemoglobinization and, despite their leukemic origin, died within 9 days after transduction; primary erythroid cultures accelerated their kinetics of erythroid maturation and increased the number of cells that reached the final enucleation step. Searching for direct Sox6 targets, we found SOCS3 (suppressor of cytokine signaling-3), a known mediator of cytokine response. Sox6 was bound in vitro and in vivo to an evolutionarily conserved regulatory SOCS3 element, which induced transcriptional activation. SOCS3 overexpression in K562 cells and in primary erythroid cells recapitulated the growth inhibition induced by Sox6, which demonstrates that SOCS3 is a relevant Sox6 effector.
Microfracture: Surgical Technique and Rehabilitation to Treat Chondral Defects (2001)

Full-thickness articular cartilage defects rarely heal spontaneously. Some patients may not have clinically significant problems from chondral defects, but most eventually have degenerative changes. Techniques to treat chondral defects include abrasion, drilling, autografts, allografts, and cell transplantation. The senior author (JRS) developed the microfracture technique to enhance chondral resurfacing by providing a suitable environment for new tissue formation and taking advantage of the body's own healing potential. Microfracture has been done in more than 1800 patients. Specially designed awls are used to make multiple perforations, or microfractures, into the subchondral bone plate. Perforations are made as close together as possible, but not so close that one breaks into another. They usually are approximately 3 to 4 mm apart. The integrity of the subchondral bone plate must be maintained. The released marrow elements (including mesenchymal stem cells, growth factors, and other healing proteins) form a surgically induced super clot that provides an enriched environment for new tissue formation. The rehabilitation program is crucial to optimize the results of the surgery. It promotes the ideal physical environment for the marrow mesenchymal stem cells to differentiate into articular cartilagelike cells, ultimately leading to development of a durable repair cartilage that fills the original defect.
The polycystic kidney disease 1 gene lies in a duplicated genomic region (1994)

The polycystic kidney disease 1 (PKD1) gene is situated in chromosomal band 16p13.3 and encodes a 14 kb transcript. The 5{prime} region of the PKD1 gene is located within a 40-50 kb stretch of genomic DNA which is duplicated several times in the more proximal region, 16p13.1. This proximal area gives rise to at least three transcripts designated homologous gene A (HG-A; 21 kb), HG-B (17 kb) and HG-C (8.5 kb). These three transcripts share substantial homology with each other and the PKD1 transcript. However, the 3{prime} 3.8 kb section of the PKD1 transcript is unique because it is encoded by a region of the gene that lies outside the duplicated area. The presence of the duplicate transcripts in all tissues analyzed has hampered attempts to clone and sequence the bone fide PKD1 gene. Comparison of cDNAs known to arise from the PKD1 transcript to those from the HG transcripts reveals that divergence of 2-3% has occurred between these sequences. To overcome the problem of the duplication, a large 15 kb section of genomic DNA has been sequenced together with several large HG cDNAs. Utilizing a radiation hybrid which contains only the 16p13.3 region and expresses low levels of themore » PKD1 transcript, we are now attempting to clone the duplicated part of the PKD1 gene by exon linking.« less
Phenotypic characteristics of human type II alveolar epithelial cells suitable for antigen presentation to T lymphocytes (2011)

Constitutive expression of MHC class I and II molecules as well as alternative co-stimulatory molecules by freshly isolated AECII render these cells a good model to study antigen presentation.
Targeting IL-34 in chronic inflammation (2014)

A second ligand for colony-stimulating factor-1 receptor (CSF-1R) with distinct biologic activities had long been implicated but not appreciated until the recent discovery of interleukin (IL)-34. IL-34 and CSF-1 signal through this common receptor to mediate the biology of mononuclear phagocytic cells. Aberrant macrophage activation by CSF-1 and/or IL-34 is associated with numerous diseases, and clinical therapies targeting this pathway are being tested. Although IL-34 and CSF-1 have distinct activities under physiologic conditions, they appear functionally redundant in various disease states. Thus, blocking the activity of both might be necessary for maximal efficacy.
Natural History of Cluster Headache‐ Part 1 Outcome of Drop‐out Patients (1982)

SYNOPSIS Cluster patients lost to follow‐up for a period of from three to eight years were the subject of this study. One hundred and forty‐nine/169 drop‐outs or their relatives were contacted via mailings, telephone calls, or professional missing‐person searchers; and questioned regarding headache status and serious illness. Of the 149 drop‐out patients, 75 (50.3%) reported no change in headache. Eleven (7.4%) had experienced a shift in headache type, that is, from chronic to episodic or episodic to chronic, equally. Fifty‐one (34.2%) had experienced a prolonged (permanent ?) remission, and twelve (8.1%) had died. Thus, the major determinants of drop‐out status included prolonged remission (longer than usual remission duration) and death (42.3%). Remission and mortality rates increased with duration of cluster disorder. Prolonged (permanent ?) remission rates were highest among patients who had previously experienced usual remission period durations of one year or longer. Mortality increased with age. Cancer mortality, however, was found to be twice that of coronary artery disease and stroke combined. There was a proportionately higher representation of women and chronic types in the cancer mortality group. Although all patients in this group had smoked cigarettes and drank alcohol, no correlation could be made between extent of these habits and site of cancer.