gebhart/patrepeval huggingface dataset:
Engineering, Expression and Renaturation of Targeted TGF-Beta Fusion Proteins (1996)

This study reports the expression, purification, and renaturation of biologically active Transforming Growth Factor-beta 1 (TGF-beta 1) fusion proteins from Escherichia coli (E. coli). A prokaryotic expression vector was engineered to produce tripartite fusion proteins consisting of (i) a purification tag, (ii) a protease-sensitive linker/collagen binding domain, and (iii) a cDNA sequence encoding the active fragment of human TGF-beta 1. The expressed fusion proteins TGF-B1-F1 and TGF-B1-F2, located in inclusion bodies, were solubilized with 8 M urea and renatured using a glutathione redox-coupled system and protracted dialysis under several experimental conditions. The purification of the recombinant proteins was achieved by binding the His-tag of the fusion proteins on a Ni-NTA metal chelate column. The biological activity of the recombinant growth factor was demonstrated by its ability to inhibit mink lung (Mv1Lu) cell proliferation and/or to stimulate proliferation of NIH-3T3 mouse fibroblasts, where purified human platelet TGF-beta 1 served as a positive control. Purified TGF-B1-F1 and TGF-B1-F2 (collagen-binding) constructs exhibited anti-proliferative activities comparable to purified platelet TGF-beta 1, but at lower specific activities. Binding of the renatured TGF-B1-F2 fusion protein to collagen was demonstrated by stable binding on a collagen-conjugated Sephadex-G15 column. The high affinity binding was also demonstrated by the binding of 3H-collagen to the TGF-B1-F2 protein immobilized on a Ni-NTA column. The TGF-B1-F2 fusion protein bound to collagen coated surfaces with high affinity but exhibited comparatively lower biological activity than the fusion protein in solution, suggesting a potentially latent configuration. Taken together, these results demonstrate that biologically active TGF-beta 1 fusion proteins can be recovered from transformed bacteria by oxidative refolding; thus, providing a means for its high-yield production, purification, and renaturation from microorganisms. Furthermore, these results support the concept that auxiliary domains may be used to modulate and/or target TGF-beta 1 for specific applications.
Comprehensive microRNA expression profiling of the hematopoietic hierarchy (2010)

The hematopoietic system produces a large number of highly specialized cell types that are derived through a hierarchical differentiation process from a common stem cell population. miRNAs are critical players in orchestrating this differentiation. Here, we report the development and application of a high-throughput microfluidic real-time quantitative PCR (RT-qPCR) approach for generating global miRNA profiles for 27 phenotypically distinct cell populations isolated from normal adult mouse hematopoietic tissues. A total of 80,000 RT-qPCR assays were used to map the landscape of miRNA expression across the hematopoietic hierarchy, including rare progenitor and stem cell populations. We show that miRNA profiles allow for the direct inference of cell lineage relations and functional similarity. Our analysis reveals a close relatedness of the miRNA expression patterns in multipotent progenitors and stem cells, followed by a major reprogramming upon restriction of differentiation potential to a single lineage. The analysis of miRNA expression in single hematopoietic cells further demonstrates that miRNA expression is very tightly regulated within highly purified populations, underscoring the potential of single-cell miRNA profiling for assessing compartment heterogeneity.
Nocturnal Melatonin Secretion in Multiple Sclerosis Patients with Affective Disorders (1993)

The pineal gland has been implicated recently in the pathogenesis of multiple sclerosis (MS), a chronic demyelinating disease of CNS. Since nocturnal melatonin secretion is low in some groups of patients with mental depression, we predicted lower melatonin secretion in MS patients with history of affective illness compared to those without psychiatric disorders. To test this hypothesis, we studied single nocturnal plasma melatonin levels and the incidence of pineal calcification (PC) on CT scan in a cohort of 25 MS patients (4 men, 21 women; mean age = 39.4 years, SD = 9.3), 15 of whom had a history of coexisting psychiatric disorders with predominant affective symptomatology. Other factors that may be related to depression such as vitamin B12, folic acid, zinc, magnesium, and homocysteine, were also included in the analysis. Neither any of the metabolic factors surveyed nor the incidence of PC distinguished the psychiatric from the control group. However, the mean melatonin level in the psychiatric patients was significantly lower than in the control group. Since low melatonin secretion in patients with depression may be related to a phase-advance of the circadian oscillator regulating the offset of melatonin secretion, we propose that the depression of MS likewise may reflect the presence of dampened circadian oscillators. Furthermore, since exacerbation of motor symptoms in MS patients may be temporally related to worsening of depression, we propose that circadian phase lability may also underlie the relapsing-remitting course of the disease. Consequently, pharmacological agents such as lithium or bright light therapy, which have been shown to phase-delay circadian rhythms, might be effective in the treatment of affective symptoms in MS as well as preventing motor exacerbation and hastening a remission from an acute attack.
Gut-Liver Interaction During Accelerated Gluconeogenesis (1985)

The effect of dexamethasone sodium phosphate on visceral organ glucose metabolism was studied in order to gain further understanding of the altered glucose dynamics that occur following catabolic states. Glucose, glutamine, and alanine exchange across the gastrointestinal (GI) tract, liver, and kidneys was determined in 25 awake dogs that were catheterized on a long-term basis during a control period and after dexamethasone sodium phosphate treatment (0.44 mg/kg/day) for two (dexamethasone 2) and nine (dexamethasone 9) days. The GI tract consumed glucose in control dogs but switched to an organ of balance or slight release with dexamethasone. Simultaneously, gut glutamine consumption increased markedly, as did intestinal alanine release. Hepatic glucose production more than doubled with dexamethasone at a time when hepatic alanine uptake was greatly increased. The kidneys demonstrated glucose balance in control animals, but released glucose with dexamethasone 9. The gut and kidneys may play an important role in the altered glucose dynamics seen in patients with sepsis and other catabolic diseases.
KEGG: Kyoto Encyclopedia of Genes and Genomes (1999)

Kyoto Encyclopedia of Genes and Genomes (KEGG) is a knowledge base for systematic analysis of gene functions in terms of the networks of genes and molecules. The major component of KEGG is the PATHWAY database that consists of graphical diagrams of biochemical pathways including most of the known metabolic pathways and some of the known regulatory pathways. The pathway information is also represented by the ortholog group tables summarizing orthologous and paralogous gene groups among different organisms. KEGG maintains the GENES database for the gene catalogs of all organisms with complete genomes and selected organisms with partial genomes, which are continuously re-annotated, as well as the LIGAND database for chemical compounds and enzymes. Each gene catalog is associated with the graphical genome map for chromosomal locations that is represented by Java applet. In addition to the data collection efforts, KEGG develops and provides various computational tools, such as for reconstructing biochemical pathways from the complete genome sequence and for predicting gene regulatory networks from the gene expression profiles. The KEGG databases are daily updated and made freely available (http://www.genome.ad.jp/kegg/).
Cd40-Independent Pathways of T Cell Help for Priming of Cd8+ Cytotoxic T Lymphocytes (2000)

In many cases, induction of CD8(+) CTL responses requires CD4(+) T cell help. Recently, it has been shown that a dominant pathway of CD4(+) help is via antigen-presenting cell (APC) activation through engagement of CD40 by CD40 ligand on CD4(+) T cells. To further study this three cell interaction, we established an in vitro system using dendritic cells (DCs) as APCs and influenza hemagglutinin (HA) class I and II peptide-specific T cell antigen receptor transgenic T cells as cytotoxic T lymphocyte precursors and CD4(+) T helper cells, respectively. We found that CD4(+) T cells can provide potent help for DCs to activate CD8(+) T cells when antigen is provided in the form of either cell lysate, recombinant protein, or synthetic peptides. Surprisingly, this help is completely independent of CD40. Moreover, CD40-independent CD4(+) help can be documented in vivo. Finally, we show that CD40-independent T cell help is delivered through both sensitization of DCs and direct CD4(+)-CD8(+) T cell communication via lymphokines. Therefore, we conclude that CD4(+) help comprises at least three components: CD40-dependent DC sensitization, CD40-independent DC sensitization, and direct lymphokine-dependent CD4(+)-CD8(+) T cell communication.
Internal optical losses in very thin CW heterojunction laser diodes (1975)

Theoretical calculations are presented showing the relationship between the internal laser absorption and structural parameters appropriate for CW room-temperature lasers. These diodes have submicron-thick recombination regions, and very small spacings between the heat sink and the recombination region to minimize the thermal resistance. The optical loss is shown to be strongly dependent on the degree of radiation confinement to the active region. In particular, absorption in the surface GaAs layer providing the ohmic contact becomes very significant when the intermediate (AlGa)As layer is reduced below about 1 μm. It is further shown that excessive penetration into the GaAs regions gives rise to anomalies in the far-field radiation profiles in the direction perpendicular to the junction plane. Proper design of the internal structure of the laser avoids large increases of the threshold current density as well as large decreases in the external differential quantum efficiency from interaction with the contact layer. The design curves presented can be used to predict the gain required at threshold for a broad range of structural parameters of interest in low-threshold laser design.
Software thermal management of dram memory for multicore systems (2008)

Thermal management of DRAM memory has become a critical issue for server systems. We have done, to our best knowledge, the first study of software thermal management for memory subsystem on real machines. Two recently proposed DTM (Dynamic Thermal Management) policies have been improved and implemented in Linux OS and evaluated on two multicore servers, a Dell PowerEdge 1950 server and a customized Intel SR1500AL server testbed. The experimental results first confirm that a system-level memory DTM policy may significantly improve system performance and power efficiency, compared with existing memory bandwidth throttling scheme. A policy called DTM-ACG (Adaptive Core Gating) shows performance improvement comparable to that reported previously. The average performance improvements are 13.3% and 7.2% on the PowerEdge 1950 and the SR1500AL (vs. 16.3% from the previous simulation-based study), respectively. We also have surprising findings that reveal the weakness of the previous study: the CPU heat dissipation and its impact on DRAM memories, which were ignored, are significant factors. We have observed that the second policy, called DTM-CDVFS (Coordinated Dynamic Voltage and Frequency Scaling), has much better performance than previously reported for this reason. The average improvements are 10.8% and 15.3% on the two machines (vs. 3.4% from the previous study), respectively. It also significantly reduces the processor power by 15.5% and energy by 22.7% on average.
V102862 (Co 102862): a potent, broad‐spectrum state‐dependent blocker of mammalian voltage‐gated sodium channels (2005)

1. 4-(4-Fluorophenoxy)benzaldehyde semicarbazone (V102862) was initially described as an orally active anticonvulsant with robust activity in a variety of rodent models of epilepsy. The mechanism of action was not known. We used whole-cell patch-clamp techniques to study the effects of V102862 on native and recombinant mammalian voltage-gated Na+ channels. 2. V102862 blocked Na+ currents (I(Na)) in acutely dissociated cultured rat hippocampal neurons. Potency increased with membrane depolarization, suggesting a state-dependent mechanism of inhibition. There was no significant effect on the voltage dependence of activation of I(Na). 3. The dissociation constant for the inactivated state (K(I)) was approximately 0.6 microM, whereas the dissociation constant for the resting state (K(R)) was >15 microM. 4. The binding to inactivated channels was slow, requiring a few seconds to reach steady state at -80 mV. 5. The mechanism of inhibition was characterized in more detail using human embryonic kidney-293 cells stably expressing rat brain type IIA Na+ (rNa(v)1.2) channels, a major Na+ channel alpha subunit in rat hippocampal neurons. Similar to hippocampal neurons, V102862 was a potent state-dependent blocker of rNa(v)1.2 channels with a K(I) of approximately 0.4 microM and K(R) approximately 30 microM. V102862 binding to inactivated channels was relatively slow (k(+) approximately = 1.7 microM(-1) s(-1)). V102862 shifted the steady-state availability curve in the hyperpolarizing direction and significantly retarded recovery of Na+ channels from inactivation. 6. These results suggest that inhibition of voltage-gated Na+ channels is a major mechanism underlying the anticonvulsant properties of V102862. Moreover, understanding the biophysics of the interaction may prove to be useful in designing a new generation of potent Na+ channel blocker therapeutics.
Tissue Distribution and Metabolism of the [ 32 P]-Labeled Oligodeoxynucleoside Methylphosphonate-Neoglycopeptide Conjugate, [YEE(ah-GalNAc) 3 ]-SMCC-AET-pU m p

T

7 , in the Mouse (1997)

Development of oligodeoxynucleotides (oligo-dNs) and their analogs as therapeutic agents is complicated by their low rate of transport across cellular membranes, which is required for interaction with the intracellular complementary nucleic acid sequences, and the lack of tissue-specific delivery. To overcome these obstacles, bioconjugates between cell surface receptor ligands and oligodeoxynucleoside methylphosphonates (oligo-MPs) have been constructed containing homogeneous, chemically defined covalent linkages. We have previously established that a model conjugate, [32P]-labeled [YEE(ah-GalNAc)3]-SMCC-AET-pUmpT7 (1), is delivered to Hep G2 cells in a ligand-specific manner, reaching a peak value of 26 pmol per 10(6) cells after 24 hours incubation at 37 degrees C (Hangeland et al., 1995). In this work, the in vivo behavior of this conjugate is explored. Administration of this conjugate to mice via tail vein injection demonstrates rapid uptake in liver to the extent of 69.9 +/- 9.9% of the injected dose after 15 minutes. Thereafter, the conjugate and its metabolites are rapidly cleared via the kidney and urine. Polyacrylamide gel electrophoresis analysis of extracts of Hep G2 cells and mouse liver reveal the conjugate 1 to be extensively metabolized. In contrast, the conjugate found in mouse urine is largely intact. These data show that this novel, biodegradable delivery vehicle represents a viable approach for the delivery of antisense oligo-MPs and other oligo-dN analogs to the liver for therapeutic and diagnostic applications.
Multiplex Detection of RNA Expression in Drosophila Embryos (2004)

We present a fluorescence-based, multiplex in situ hybridization method that permits the simultaneous detection of five differently labeled antisense RNA probes and up to seven differ-ent transcripts in a single Drosophila embryo. We also show that it should be possible to increase the number of detected transcripts substantially with nascent transcript multiplex fluorescent in situ hybridization. These multiplex methods fill a current technological gap between high-resolution in situ hybridization with one or two fluorescently labeled probes and low-resolution but genome-wide microarray RNA profiling and should be of great utility in establishing gene networks.
Early Detection of Apoptosis Using a Fluorescent Conjugate of Annexin V (1997)

Apoptosis of mammalian cells is accompanied by various morphological changes including nuclear condensation, DNA fragmentation and cell surface changes. Methods developed over the past few years have focused on detection of DNA-associated changes that occur rather late in apoptosis. However, detection of apoptosis at early stages, before gross morphological changes, is critical for understanding the pathways of programmed cell death. In this report, we describe a rapid and reliable assay for detecting early stages of apoptosis. This assay is based on the observation that soon after initiating apoptosis, most mammalian cell types translocate phosphatidylserine (PS) from the inner face of the plasma membrane to the cell surface. Once on the cell surface, PS can be specifically detected by staining with fluorescein isothiocyanate (FITC)-labeled annexin V (annexin V-FITC), a protein with a strong, natural affinity for PS. Using this assay, we have detected apoptotic cells in culture, in real time, using fluorescence microscopy and flow cytometry. In combination with vital dye staining, the progressive stages of apoptosis were observed. PS redistribution occurs earlier than DNA-associated changes and membrane leakage. In addition, PS externalization occurs during apoptosis induced by a variety of stimuli. Therefore, the annexin V binding assay provides an excellent indicator for the early stages of apoptosis.
Fish-like underwater microrobot with 3 DOF (2003)

It is our purpose to develop an underwater microrobot that has the characteristics of flexibility, driven by a low voltage, good response and safety in body. We propose a prototype model of an underwater microrobot utilizing an ICPF (ionic conducting polymer film) actuator as the servo actuator to realize swimming motion with 3 DOF. A biomimetic fish-like microrobot using an ICPF actuator as a propulsion tail fin and a buoyancy adjuster for a microrobot swimming structure in water or aqueous medium has been developed. The overall size of the underwater microrobot prototype shaped as a fish is 45mm in length, 10 mm in width and 4 mm in thickness. There is a pair of fins and a buoyancy adjuster. The characteristics of the underwater microrobot is measured by changing the frequency and amplitude of input voltage. The experimental results indicate that the swimming speed of the proposed underwater micro robot can be controlled by changing the frequency of input voltage; the moving direction (upward or downward) can be controlled by changing the amplitude and the frequency of input voltage.
Kinetically stable complexes of alkali cations with rigidified calix[4]arenes: synthesis, x-ray structures, and complexation of calixcrowns and calixspherands (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTKinetically stable complexes of alkali cations with rigidified calix[4]arenes: synthesis, x-ray structures, and complexation of calixcrowns and calixspherandsPieter J. Dijkstra, Jos A. J. Brunink, Kjell Erik Bugge, David N. Reinhoudt, Sybolt Harkema, Rocco Ungaro, Franco Ugozzoli, and Eleonora GhidiniCite this: J. Am. Chem. Soc. 1989, 111, 19, 7567–7575Publication Date (Print):September 1, 1989Publication History Published online1 May 2002Published inissue 1 September 1989https://pubs.acs.org/doi/10.1021/ja00201a045https://doi.org/10.1021/ja00201a045research-articleACS PublicationsRequest reuse permissionsArticle Views803Altmetric-Citations195LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Isolation and characterization of the gene encoding phosphoenolpyruvate carboxykinase from Saccharomyces cerevisiae (1989)

The yeast PCK1 gene coding for phosphoenolpyruvate carboxykinase (PEPCK) was isolated by functional complementation of pck1 strains from S. cerevisiae. Only one copy of the gene was found per haploid yeast genome. An RNA of about 2 kb which hybridized with a DNA probe internal to the PCK1 gene was found only in cells growing in non-fermentable carbon sources. Yeast strains carrying multiple copies of the PCK1 gene showed normal catabolite repression of PEPCK except those carrying the shortest insertion complementing the mutation (2.2 kb) that presented an altered kinetics of derepression. Catabolite inactivation was decreased in strains transformed with multicopy plasmids carrying the PCK1 gene.
Von Willebrand's disease in dogs. (1984)

Von Willebrand's disease, the most common, mild, inherited bleeding disorder of animals, is an autosomal trait generally causing high morbidity and low mortality and affecting many breeds of dogs. Clinical signs include hematuria, epistaxis, gingival or genital mucosal bleeding, lameness, and prolonged bleeding from cut nails or wounds. Concurrent hypothyroidism exacerbates the disease. Affected dogs and carriers should not be bred or should be tested for von Willebrand's factor before breeding. Treatment involves IV infusion of fresh whole blood or plasma, at 3-5 ml/lb, with topical use of hemostatic compounds, and avoidance of drugs that interfere with hemostasis.
A Novel Biological-Based Assay for the Screening of Neutralizing Antibodies to Ricin (1999)

A novel approach to screen hybridomas producing antibodies directed against ricin was developed. Anti-ricin antibodies were produced and characterized based on protection of Sp2/mIL6 myeloma cells and in vivo studies demonstrating neutralization of the toxic effects of ricin in mice. During the production of hybridomas, cells were plated in media supplemented with hypoxanthine, aminopterin, and thymidine supplement (HAT), HAT + ricin, or ricin. Three hybridomas, designated HRF4, HHRD7 and HHRD9, were selected from the media supplemented with ricin and were shown to produce antibodies directed against ricin. Intraperitoneal injection of hybridoma supernatant containing anti-ricin antibodies combined with 0.5 microg ricin (a toxic dosage) protected Balb/C mice from the deleterious effects of the ricin. Hybridoma, HHRD9, did not contain high titre antibodies to ricin but appeared to neutralize the toxic effects of ricin in mice.